General

Assuming your focus is bossing (like most players), when planning your end game Hyper Stats, prioritize:

Total damage = Boss Damage > Max Crit > Min Crit > Def. Ignore > Crit rate > Main Stat > Status Resist

Total and Boss Damage, Max and Min Crit should be maxed eventually, I believe we can all agree on that. Total Damage and Boss Damage stack additively, so they are pretty much the same. Max Crit hyper stat gives more than the Min Crit hyper stat, so level it first.

Def. Ignore is amazing at bosses like C. Vellum or Lotus and can free up potential lines on the Emblem, but otherwise it isn't a top priority and doesn't need to be maxed.

You preferably want to reach max crit rate while saving Hyper Stats sp (classes with high base critical rates have a HUGE advantage here) so you can use it elsewhere, but get as much crit rate as you need.

Main Stat power diminishes the more %stat you have, since it is NOT affected by it, that's why I put it so low on the list, although it is still a respectable increase (150 on top of a 15k stat is still a 1% increase in damage) in damage otherwise, but this is 'end game planning'. Also, RIP Xenon.

Status Resist is situational and most characters can actually cap it without using SP. Sure it might take some effort, but it is far easier than trying to level a 200+ character because you need more sp.

The ideal order to level them up, however... Still trying to figure that out. It's clearly not worth to simply dump all your sp in one skill when you could level multiple at the same time, so in the end it might be worth it to simply level up the lowest level skill that isn't already at the planned level.

@earlier: I'll test it in-game then, thanks!

@snoopypig: Apparently it doesn't work with % stat.

@twopointonefour: why o-o

@snoopypig: You may want to consider dropping the STR.

I went with leveling up the skill that give me the best damage boost to the points I invest in, although it's a greedy algorithm it should give quite a good result.
I wrote myself a little java program to do that calculation, the output was:
Leveling up: TD% from level 0 to level 1. Points left: 419.
Leveling up: Boss% from level 0 to level 1. Points left: 418.
Leveling up: PDR% from level 0 to level 1. Points left: 417.
Leveling up: Crit Rate% from level 0 to level 1. Points left: 416.
Leveling up: STR from level 0 to level 1. Points left: 415.
Leveling up: Max Crit % from level 0 to level 1. Points left: 414.
Leveling up: Min Crit % from level 0 to level 1. Points left: 413.
Leveling up: TD% from level 1 to level 2. Points left: 411.
Leveling up: Boss% from level 1 to level 2. Points left: 409.
Leveling up: PDR% from level 1 to level 2. Points left: 407.
Leveling up: Crit Rate% from level 1 to level 2. Points left: 405.
Leveling up: STR from level 1 to level 2. Points left: 403.
Leveling up: Max Crit % from level 1 to level 2. Points left: 401.
Leveling up: Min Crit % from level 1 to level 2. Points left: 399.
Leveling up: TD% from level 2 to level 3. Points left: 395.
Leveling up: Boss% from level 2 to level 3. Points left: 391.
Leveling up: PDR% from level 2 to level 3. Points left: 387.
Leveling up: Crit Rate% from level 2 to level 3. Points left: 383.
Leveling up: STR from level 2 to level 3. Points left: 379.
Leveling up: Max Crit % from level 2 to level 3. Points left: 375.
Leveling up: Min Crit % from level 2 to level 3. Points left: 371.
Leveling up: TD% from level 3 to level 4. Points left: 363.
Leveling up: Boss% from level 3 to level 4. Points left: 355.
Leveling up: PDR% from level 3 to level 4. Points left: 347.
Leveling up: TD% from level 4 to level 5. Points left: 337.
Leveling up: Boss% from level 4 to level 5. Points left: 327.
Leveling up: Crit Rate% from level 3 to level 4. Points left: 319.
Leveling up: STR from level 3 to level 4. Points left: 311.
Leveling up: Max Crit % from level 3 to level 4. Points left: 303.
Leveling up: Min Crit % from level 3 to level 4. Points left: 295.
Leveling up: PDR% from level 4 to level 5. Points left: 285.
Leveling up: Crit Rate% from level 4 to level 5. Points left: 275.
Leveling up: STR from level 4 to level 5. Points left: 265.
Leveling up: Max Crit % from level 4 to level 5. Points left: 255.
Leveling up: Min Crit % from level 4 to level 5. Points left: 245.
Leveling up: Boss% from level 5 to level 6. Points left: 230.
Leveling up: TD% from level 5 to level 6. Points left: 215.
Leveling up: PDR% from level 5 to level 6. Points left: 200.
Leveling up: Crit Rate% from level 5 to level 6. Points left: 185.
Leveling up: STR from level 5 to level 6. Points left: 170.
Leveling up: Max Crit % from level 5 to level 6. Points left: 155.
Leveling up: Min Crit % from level 5 to level 6. Points left: 140.
Leveling up: Boss% from level 6 to level 7. Points left: 120.
Leveling up: TD% from level 6 to level 7. Points left: 100.
Leveling up: PDR% from level 6 to level 7. Points left: 80.
Leveling up: Crit Rate% from level 6 to level 7. Points left: 60.
Leveling up: Boss% from level 7 to level 8. Points left: 35.
Leveling up: Max Crit % from level 6 to level 7. Points left: 15.
COMPLETE

I do want to stress that this is specific for my class and stats.

@mudkippiratez: powerbomb meant Hyper Skill Passives, which are becoming Hyper Stat.s

Hyper Stats are being revamped not Hyper Skills.

Stat, Crit, Boss, Damage?

So you can see what you can afford: http://jsfiddle.net/MegaScience/au9v6LhL/embedded/result/

Throw health out the window, i'd reccomend status resist if you boss, crit rate if you need it, damage unless you have a lot (like Phantom) boss damage and the min and max crits.