Is having each planet be balanced a good idea at all?
Either way works, specialized or generic. One thing you need to consider is the number of habitables in your game. If each race only has a few planets, then losing one is a big deal. In a gigantic/abundant game with max habitables, you can lose a number and not worry about it, even if they're specialized. I play mostly gig/abun so my comments are oriented toward that.
How do you balance out concentrated planets otherwise?
I like to take advantage of what a planet has to offer. Higher class planets are my military production workhorses. Lower class planets are my money makers, but that's not always the case. Bonus tiles can determine whether a planet goes production or economy. I build a few research planets as well, but not too many. A planet with a lot of research bonus tiles may get all labs and a tech capitol, Research Coordination Center (DA), or Omega Research Center.
What's your strategy on fleet composition? Or do you just build one massive cruiser.
Build the biggest hull fighters I can. I run a balance of engines, defenses, and weapons, but defenses are a lower priority until I have a lot of defense tech. In DL I fleet them. The battle system does not favor fleets in DA so I run them solo in that game. Transports are cheap throw-aways consisting of a cargo hull with nothing but engines and a transport module. I do escort them with fighters sometimes, but not fleeted. My transports are totally defenseless otherwise. They totally rely on speed.
How do you handle early-game invasions of your planets?
I don't defend them. I give them up because for every one they get, I can use that firepower to take 3 of theirs. Also, I try to intercept enemy transports with fast fighters before they can do any damage. Eyes of the Universe and scout ships are key for this.
When do you start building defenses around your planets?
I don't. Like I said, I use that firepower for offense. The thing is, the AI is pretty slow about taking planets. I can pretty much waste them before they can take enough of my planets to really hurt me.