Just some comments about 0.4.6E. Toyed quite a bit with the Dominion and Federation. As far as ships go:
Federation: Respectable offensive and defensive power all around, IMO. Where the Feds really kill is that there's a fancy trick for every occasion. Disabling, attack boosts, repair / replenish aids, group aids. Everything and the kitchen sink, provided you do the research. Not to mention boosts to old workhorse ships to make them even more useful, i.e. Miranda. Utility is Starfleet's game, and their Capital Ships, esp. the Galaxy and Sovereign are tough to bring down in a battle.
The other thing that really must be said about Starlfeet ships is that with proper measures, they recover very, very fast to push on for the next attack. Repairs can be done quickly, but where Fed ships dominate is shield recovery. It really doesn't take long to have a once battered fleet ready for the next fight. Pop in a few frigates for replacements. Over the course of a handful of minutes and decent facilities, the entire fleet's Hull & Shields are at 100%. Once the Feds start a steamroll, it's hard to stop with the cross supporting ships and their persistency.
Not to mention the swarms of fighters/bombers a Fed fleet will have. It's like a whole other fleet free of charge acting independently in the battle.
Lots of cool stuff with the Feds. It also makes playing them very easy.
Dominion: Quite a few differences from Starfleet's ships. The Breen frigate and assault cruiser are key points in a Dominion fleet because of their debilitating effects. They play a big role in breaking up the overabundance of Federation special abilities. To make the Breen ships even more important is the stark fact that Jem'Hadar non-capital ships have essentially no utility.
Jem'Hadar warships... across the board their firepower is respectable. Their frigates and cruisers have average staying power. Very little special abilities, if at all. I really wanted to get a much larger Jem'Hadar ship count, but their Cruiser and 1 frigate type just failed to even be respectable considering their costs. The only non-capital Jem'Hadar ship I favored was the inexpensive, fast Dominator / Bug Ship. They can be cheap fodder for Kamikaze attacks. You can get alot of them. And on the pursuit, the only light ship / frigate that comes close in performance in that role are Klingon B'Rel BOPs.
Now, Jem'Hadar Capital Ships... their claim to fame is sheer attack power and toughness. Their first accessible Cap Ship is a carrier with 15k shield strength, and with a bit of work, minor group buffing. Not to mention a way to keep those pesky Cardassians in check. Its firepower is considerably nice early on and only gets overshadowed about mid-game. Even with the more massive Jem'Hadar ships being introduced, I liked having a few of the carriers for the group aids. The big ships of the Dominion, compared to Starfleet, have very little utility or cross support. They're mostly geared for the single ship performance, namely churning out hot death. Very little team support. Still, the middle of the cap ship lineup are very tough by themselves.
The siege specialist of their Capital Ships can also access, with a bit of experience, Opening Salvo. Very good attack in whittling down large frigate groups and wearing down a bit anything else that survived in the area.
Then there's the Enslaver, the biggest ship the Dominion has. Heavily armored and shielded. Excessively armed to the teeth. Can access Opening Salvo early on. Their highest ability, "Victory is Life!" is a very nice offensive boost to any nearby Jem'Hadar ships. A pair of Enslavers with maxed out Opening Salvo are absolutely amazing in clearing the field of enemy frigates as well as damaging badly anything else that didn't blow up. These became easily my most sought after and most numerous of Dominion cap ships. Very, very tough and hard hitting. Top of the priority list in attaining.
From my Dominion fleet selection, I tended towards Enslavers, a Carrier (for group aids), a bunch of Breen ships, and lots of Dominators. What makes the Dominators important is the smaller footprint they leave in Supplies required. A full compliment of Enslavers in the war are extremely costly in supplies.
Oh, and the Cardassians in the Dominion lineup. In the previous version, I did get a bunch of them. But they rebel and that left a bad taste in the mouth. I haven't given them a try with this version. I have no need for untrustworthy forces.
The last thing I have to say is a sharp contrast in fighting compared to the Federation. The Feds can regroup and be ready to go with 100% hull and 100% shields after barely any waiting. Very easy to attack, attack, and attack again in a short time span. The Dominion can't. Repairs take longer compared to the Feds. And shields take FOREVER to recover. The hull repair rate I can live with but the poor shield recovery is a detriment. Very hard to maintain the momentum of an offensive against determined resistance if you are playing with the Dominion. If the fighting is tough, even the big shields of Enslavers get worn down. It's a very long wait if you want to send your Dominion fleet to the next fight with recovered hull and shields. But in a campaign you may not have that luxury. Sometimes you have to push because of a strategic opportunity, and doing it with your fleet's surviving ships at poor shield strength. The frigates are easy to replace, but I cringe and hesitate when I have to keep pushing again and again with my expensive and highly experienced capital ships in a weakened shield state.