First of all I love the difficulty of the flood and i'm not suggesting that get changed. However the tactics to defeat them revolve entirely around 3 units in the public build and I would imagine 5 in the dev build, at least until the day forerunners get implemented (far away and unrelated).
As UNSC you essentially get your econ rolling and then turtle up with anchors and stalwarts at your border planets, and eventually you make an entire fleet of stalwarts and steamroll the flood planet.
Covenant the tactic is largely the same just substitute in pickets and salvation's.
I would imagine both factions titans will inherit the salvation's immunity to flood control which is great now we can use a grand total of 5 ships. So what i'm proposing is when the strident gets released give it the immunity perk which lore wise would work (built post war when spartan's were readily available plus being tied to the infinity which was jam packed with spartans) plus energy shielding (as far as i know shields conferred immunity to flood infection until they were depleted(think elites in halo 3) this would give each faction 3 ships that could be used against the flood.
Another possible idea would be a timer upon infection to scuttle larger ships(cole protocol, pillar of autumn detonation,etc...) I mean in a ship as large as the Thermopylae you would think at-least one person or at the very least the ai would think to damage critical systems the flood might be fast but the instant assilimation of 1000's of people on such a large vessel is highly unlikely.
Finally on the flood side of things i loved the addition of the pure form carrier and the planet guardians are nice to. actually i think the flood are fine unless it would be possible to implement a gravemind as a titan of sorts or possibly a starbase for the flood planet. maybe even a mere defensive structure (prevent warping out or increase charge speed due to mental influence)
The mods Great looking forward to whatever you do but these are a few additions which i think would allow for more versatility when fighting the flood. as far as I know they are within the limits of the sins engine and would fit lorewise and be balanced.
(if these changes are incredibly unlikely to happen could someone give me pointers on how to give the salvations immunity perk to other ships?)