Phew, well, this is going to be a tough comparison..
Well, as far as balance - it sounds like you're going to play mainly single player, in which case Sins is set up so that every ship has a use in fleets. Some are naturally weaker than others, but they get special abilities unlocked through research that keep them useful. As an example, the Advent's light frigate is the starter unit that doesn't take long to get out-matched in firepower and survivability, but it unlocks an ability that steals antimatter from enemy ships and feeds it to yours, allowing you to use more abilities.
For replayability - the largest Sins games won't take as long as the largest Civ4 games, probably. There are a lot of maps, and there are various random presets. You can make a Random Huge (~100 planets, 5 stars), or a Random Huge-Single Star, which crams fewer planets into a single star system. There's also a built in map generator - you set up a bunch of presets, and it randomly spits out a map for you (you can save these). So if you like sandbox, Sins can always keep you entertained since you never have to play the same map twice.
A notable difference of course is that since Civ4 is strictly turn based, it gets added depth in some aspects. And since Sins is real-time, it has to make do with lighter version of these, notably diplomacy and colony management. Sins is definitely geared towards warfare, and each race has a unique tech tree so that already limits some options. You can't trade techs, and the only victory condition is winning by military means (though you can ally with AIs and achieve an allied victory). You can, however, trade with your allies by securing trade treaties, which make your trade ships use your ally's trade ports and make you extra $$.
I don't know, because the games are two different genres it's really hard to say which is better. Sins is deeper than any other real time strategy game, but it's not as deep as a real turn based game so there's a bit of apple/orange stuff.
