Never been an issue for me, personally, either in GalCiv or Civilization or any other 4X that doesn't feature manual control of battle resolution.
If it's a sticking point for you, I fear you may be disappointed, as the devs have frequently confirmed that there are no plans for manual control of battle resolution. As they have pointed out, on larger maps it's entirely possible for the player to have 30 or more battles in a single turn. Manual control simply isn't practical.
My friend I knew exactly what to expect with GC3. If combat alone was a sticking point I wouldn't have stuck around after GC2. I put over a 1000 hours into GC2 and I've been a Stardockian since then. I didn't fall in love with the series for it's combat, which should be a given for any of us here as combat has never been the game's strong suit, but rather the whole 4X package. With a game like Civ: Beyond Earth though depending on how you view it, you could say even it has controllable battles because you're just clicking on your troops and then clicking on what you want them to attack. More or less same here.
As for the larger maps and how many battles you have to fight, with them being both controllable Or
auto-calculated it's a moot point and solely the players "opinion" on how many is too many to do your-self. The same could be said for any war strategy game on a large scale. In Total War or even in old school MoO2 I'd often do 10 or 20 battles per turn and not bat an eye. A long term player isn't going to do every little battle or a battle they know for sure they'll win manually anyway, but they'll do every "important" battle manually.
Even for those of us who want controllable battles in Gal Civ with knowing what Gal Civ is, none of us would be wanting or expecting anything as in depth as Total War anyway. Hell I'd be happy with just being able to click on a ship in the battle viewer, then click on it's target and watch it go. It doesn't need to be any more in depth than that as the rest of the depth is handled in how you build your ships and fleet composition and ship roles/classes. I don't think any of us wanting manual battles would expect a total overhaul of the battle system, nor want one. I don't think any true GC fan is here just for the battles. We're here for design choices. For strategic choices. For in depth research and planning how to grow your empire every time you start a new game. Will you be a war monger this time or will you go for that galactic peace victory? That's the beauty of it. Not the battles. The depth is everywhere in this game and it's the whole package that completes the big picture. As long as the auto-calculate is always there, how many battles the player choses to play through and how many they decide to auto is always left to the player. No-one is saying take out auto-battles or force the player to do every one of them manually. Then the player would be Required
to do every battle and that would get monotonous in any large strategic game, not just here.
Personally I fell in love with GC because of the total package and what I could do with it, the customization. I've never finished a story campaign in GC. Don't get me wrong I like the game's normal races, they are well designed, fleshed out nicely, and they have great AI personalities I enjoy playing against. I know the lore but that's only from reading information screens and not so much because I care about the story. It's a strategy sandbox so technically you make the story up as you go along colonizing planets or going to war with one species or another, or making peace with one species or another. To me every map is a blank story I write as I play.