Let's presume the Infinity's original intentions were as a plot device. Is this a problem? No. Within the context of the Halo universe, the Infinity fits in just fine. Its not ridiculously OP and it has a decent enough back story. Same deal with the Didacts ship. Of course it was relatively incredibly powerful and large; it was Forerunner.
The plot device-class was only seen once even though it wasn't a special ship like the Infinity or the Didacts. The plot device would've led the main fleet at Reach and would've been present at the Battle of Earth. Why would Regret take a CAS when he could take a plot device and why didn't Truth's fleet have a plot device? Why is the only mention of the plot device on Reach. Not to mention, it was used in a stealthy manner. That ship was NOT made for stealth. The plot device is also ridiculous in terms of size because it is Covie, not Forerunner (the Infinity is the perfect size for what it is).
Also, the plot of Halo Reach is shitty and canon-breaking to begin with, so the default view is to look down upon anything that comes out of it anyway. Burden of proof is on the plot device
Technically, everything is a plot device. But most fit into the lore pretty well. Sabers go under the radar because they fit in. Spartans and the Infinity have a well developed backstory and are pillars of the lore. The plot device was shoved into Reach to make the story work then dropped from existence.
It should be noted that the Covenant Supercarrier Sublime Transcendence was featured in the books First Strike and Ghosts of Onyx. So that in addition to Long Night of Solace makes two canon plot device-Class supercarriers. It wasn't necessarily shoved into Reach then dropped out of existence, as it was I suppose lazily designed in model then put in. From a story standpoint I can reason why the Covenant would do what they did, though it sort of stretches it considering for gameplay purposes you can't just have the player try to fight starships as a spartan, what with needing a reason for the Covenant to come to the ground and all (Forerunner artifacts etc) besides disabling SMAC ground generators. I don't think there would really much more to this issue if Bungie would have just given it a little different model since I don't remember if it really was described in those two books.
As far as why they exist, why there are only two of them that we know of, and why then wouldn't they be the high prophets flagships?
1. Probably just because they could build them to see how far their engineering could go. As superweapons or such.
2. It was also likely very costly and unnecessary compared to the other ships they could make for the same cost, so they didn't make that many of them.
3. It seemed like a matter of situation. The books I mentioned outline major Covenant investigations into potentially dangerous Forerunner stuff, perhaps the ship was a gift to the supreme commander and that just happened to be the fleet chosen, maybe it just happened to be the one the main characters found...they exist and they were there. By the time any high prophets were into any highly dangerous scenarios such as when the Covenant were at Terra there probably were none left (not to say such vessels could not have been used prior by them timeline speaking). Besides, Truth was on the Keyship at that point so he didn't want such a vessel since they were nearing the end anyway.
Anyway...humbly addressing the good hosts now.
In comparison to the titans in SoaSE: Rebellion, I think such vessels are actually comparable in size when compared with capital ships. Such as the TEC rebel titan compared to their battleship in size. When looking at the supercarrier and assault carrier they seem to follow such a comparison; so I don't really see how that is much of an argument to be honest. And if you hated the model so much, then I suppose you could make a unique and fitting one yourself for it, though naturally I can see how the idea is rejected due to the perceived needless extra work. And considering you are putting Mantle's Approach in the game from the screenshots of the textured model, a ship that is almost 14 times the size of the Covenant supercarrier...that argument about size just sort of falls apart on me. Not to mention the armour, shields, and firepower differences between the two...
Then of course, other mods (but are not yours, I know) have comparable ships such as superstar destroyers and Yuuzhan Vong worldships and those work fine ingame and are comparable in size to the Covenant supercarrier. And again if the Didact's flagship is going in the game, then surely you would put the fortress-class vessels in the game too right; and those things are two to four times (roughly) the size of the that supercarrier. At the very least you could just size down the thing as you say you are going to do with Mantle's Approach. I'm sure even if not in the "correct" proportions as it were, it would still be fine.
And if you are worried about balance...well you said you wanted to stick closely to the Halo canon right? Considering the differences in technology, a high tier (but not fortress) forerunner capital ship (or two) is probably comparable to the plot device in terms of power despite any assumed size differences they might have. Thus inadvertently, you might probably stick a power in the game that is equivalent to that supercarrier anyway, thus perhaps defeating the purpose of trying to exclude it. And if a titan, then its not like they can build more than one unless you want players to.
Then with respect to the UNSC well...canonically they are quite outmatched for various reasons despite strengths to overcome that in time; but then that is the charm of the mod isn't it? Fighting against overwhelming odds and doing everything you can to outwit, outplay, and defeat your opponents playing to your strengths and their weaknesses? Sounds like the UNSC all right, not to downplay Covenant or Forerunner tacticians however. Come to think of it actually, it is probably easy to set the game so that multiple titans can be built for specific factions...such as the UNSC Infinity actually being an official new class of ship lorewise...infinity class...which could help with balance if you see where I am going with that.
Considering what I have seen in both the comment sections on Moddb and posts and topics here on this site over the past two years of lurking, these arguments are just going to keep cropping up by obnoxiously irritating posters such as myself unless you guys write up an updated FAQ in places explicitly outlining every single reason as to why your reasoning on your choices. and at the same time still being open to criticism. Even then, I doubt any fleeting hopes will die from that, as perhaps years from now such things will still be desired for the sake of completeness...and maybe at the least after the mod has its official or final release however long off that is from now, you might have a change of heart. If not, then maybe someone else might...because I can see how it could work even in terms of balance if sufficient effort and passion is put in; and from what I have seen, you guys have a great deal of those. Heh, then God forbid what could happen if even more powerful ships and weapons are revealed in future Halo lore then to be somehow expected to be put into this mod...
At the end of the day though, it is your mod and there is little I could say to change that. Though I respect your decisions and mostly agree with them, when it comes to additions like this I must be honest and say that I just find your (scattered) reasonings to be very arguable. Even though the mod is in just a pre-alpha or alpha state at the moment, I must say I am very much enjoying what it has to offer, this mod has been in development since what 2007? That tells me either one of two things: you are all so busy that you do what you can with what time you have and that is why it is "only" in pre-alpha (or alpha) at this time and are not willing and/or able to work on it as much as you would like (perfectly understandable), or this is one of the best mods ever created due to the sheer amount of polish and work gone into it over such a period of time for a mod and it is "only" in pre-alpha (or alpha).
I wish you would humor me, but I will not make demands when you offer this for free (I wouldn't do such a thing even if it was paid) and no matter what I say it just won't matter...its like that Kraken fellow said: "No discussion about it will change that."
EDIT: I'm sad because no one has acted on my attempted discussion now, instead complaining about UNSC infinity Shields being too strong or something.
The Machine is strong. We must purge the weak, hated flesh and replace it with the blessed purity of metal. Only through permanence can we truly triumph, only through the Machine can we find victory. Punish the flesh. Iron in mind and body. Hail the Machine! - Paullian Blantar Iron-Father of the Kaargul Clan, Iron Hands Chapter.
We are born for a darker purpose than that of mere existence. There will come a time when stygian night never ends, where dead stars will spread before us like islands that slumber on the ocean, and when the beings that hid like shadows will feed on us forever. - Adept Corteswain at the Omniastery of Selethoth, shortly before his disappearance.