>>23261964Sky is definitely worth it, I would recommend if for its additional postgame, which is all awesome.
As for gates, yes the roster is limited, but you don't really notice it that much until you want to catch everything, (There are still 144 Pokemon in the game, so it's about as sparse as most regions in the main series until postgame) and the game itself is actually pretty sweet. (It's just not as awesome as Sky was.) So, if you want it, may as well get it! There's no sense avoiding something you want because of something that is reasonably inconsequential.
Etrian Mystery Dungeon is also quite a good game, (So far) so it doesn't matter which you choose, you'll probably end up liking either.
Etrian Mystery Dungeon also has quite a bit more complex dungeon crawling and mechanics, so you can stretch limited resources very VERY far if you play it well... So it becomes much more strategy-based in some places.