Just reached level 99, and not sure what to do? This page will helpEdit

After reached 99 I suggest you finish the main story and discover all areas. And finish the Chaos Castle.Edit

Next you will want to tackle the tower of trials to get pro credits, the tower is the very best way to get pro credits becuase the monsters there are above 99, and everytime you complete a floor you get extra points, and every time you beat a boss floor at least 1 pro credit.Edit

This table shows what the best upgrades to put your pro creditsEdit

Healing Rate This is great because your health and AP come back fast so you dont need to use items, and you get back in the fight faster to keep up your chain.
Enhance Duration This is great because you dont need to keep using AP to keep buffing yourself, and using say, Skill up lvl 3 could last 2 full boss fights (and a couple a rooms after that)
HP Boost Feel horrible when you're not paying any mind and you get 1 hit KO'ed? Well get your HP up and thats a thing of the past.
Movement Speed This one is not dire thats why I put it at the end, This is so you can run far enough away, then stand still to heal while in the middle of a fight (make sure you un-target first)
Enfeeble Resistance This one kinda is pointless, but could be useful if you maxed the credits on it. Enemies can already miss the enfeeble, this is just an extra F-U to the enemy.

The other upgrades I feel are pretty pointless (combat wise) except for AP boost but thats more trouble when healing.