Are cocos2d-iphone and cocos2d-Android the same thing? in other words, can I make a game once and deploy it to both devices?
Also, for Android, "overall" what is the best isometric game engine (cocos2d or andengine)?
I want make an isometric mutliplayer game that can run on both Android, iPhone and web. I understand that might be possible with the two engines listed, but I need to start somewhere. I took a look at Unity but I think it will be easier to start with 2D vs 3D.
Are cocos2d-iphone and cocos2d-Android the same thing? in other words, can I make a game once and deploy it to both devices?
No, they are not the same. You certainly can't deploy from one to the other. Have a look at Cocos2d-X, I don't know how it works, but it's designed to be cross platform.
Also, for Android, "overall" what is the best isometric game engine (cocos2d or andengine)?
Our office creates both iPhone and android games, the iPhone department uses Cocos2d, the Android department uses AndEngine. This is a subjective question though, you decide which is 'better'.
With regard to Unity, it provides a powerful basis for creating games, but from what I've heard, they quickly become large apps and will likely hit the 20MB limit for downloading apps on WWAN (at least in UK, not sure on other countries), quickly. Consider this if when considering Unity.