Would firstly like to start this post off by saying that I've been a long term sins fan, since vanilla sins and it's easily my favorite game. Hats off to Ironclad 
Now onto Rebellion. I like what I see so far, I put off playing the game until I finished my last exam and have only had a couple of play throughs as TEC rebels and Vasari Loyalists.
TEC rebels I found to be perfect, the titan is a vehicle of pure hatred and I love how it lights up with overcharge and starts smashing an enemy fleet apart left right and center. The ability to ally with the rebels and pirates makes them a great offensive faction.
I liked the idea behind the Vasari loyalist faction but think they need some work. The attitude behind them seems to be "we really don't have time for this s*** anymore and are just going to go through you". However, their titan didn't punch as hard as I think it should. I didn't really use the in system jump ability, apart from to chase stragglers down. On the other hand I found maw hilarious (in a good way) when it just inhaled a chunk of the enemy fleet and gave me cash. I don't really get how desperation works, can somebody explain? The ability to spawn a phase stabilizer was really nice as you could keep pouring reinforcements into the battle but think the cool down needs to be reduced somewhat.
I'd like to see the titan act as sort of a "maintains your fleet size whilst reducing theirs", so although it may not be able to stand up to another titan it would be a a formidable foe with a supporting fleet. Maw and fleet beacon fit into this perfectly but I think in system jump should be replaced with a weapon ability of some sort. An idea I had would be called "experimental phase missiles" which would launch a small volley of phase missiles packing nuclear payloads, that upon detonation on the hull would do enough damage to wipe out unlucky frigates and cruisers but give capital ships a serious head ache. If they detonate on the shield they just take that offline, keeping that ship in play.
I'd also like to see the last weapon upgrade on the titan give it access to normal phase missiles (so a fifth weapon system) as I can't believe that the vasari wouldn't fit their most effective weapon systems on their death machine.
Something else that I thought could be quite nice for the loyalists is a research option for the siege frigate, replacing their siege lasers with a diminished version of the level 6 death egg ability, where they suck up resources from the planets instead of bombing them relentlessly. However, it should slow down the planet capture process and not work as well as the death eggs ability. It would fit in nicely with the lore of the loyalists desperately scrounging as many resources as quickly as possible at any opportunity.