similar to my previous question concerning activating HP spheres before aquiring break HP limit, I would like to know if you guys recommend to get the anima and magus sisters as soon as possible.

I'm levelling Yuna up quite a lot, so I was just wondering: if I got Yuna through the whole sphere grid, with every node activated and only THEN get the last 2 aeons, won't I lose the oppertunity to level those aeons up even further?

No, as their stats will always be based off of Yuna (if they're high enough). Get them anyway though. They can help with the tough battles.