the special/magical abilities are the ones you really have to watch for order. Note that changing the type of magic/poisoning on a pet that already has magic/poisoning can (and usually will) change the options for special abilities (As well as eliminate or render frozen certain skills), and taking some mid-level abilities eliminate the chance of taking a 2nd ability. Look for the threads on this to get a better explanation. If a pet already has abilities, choices can sometimes screw up/negate existing ones.
For Resists, note there is a cap of 80 for raising an individual resist to, and that there is a cap of something like 360 for all 5 resists combined. And, overcapped resists count toward that amount. So pick which resists to raise by the order you want them highest, as you may not have any points left to put into the last one, or possibly even the 4th one.
For stats: Raise dex to 150, then raise STR to your desired amount. All INT does for a pet is possibly affecting the focus/med formula, so there's little pressing need for more INT for med (do consider using focus and Med powerscrolls, though). There is an overall cap, but it's not that big an issue as long as you do the dex and str first.
For derived stats: HP, Stamina and Mana are no longer tied to their corresponding stat. Raise stamina to 150. HP and Mana should be done based on your pet's abilities (as even things that don't use mana when players use them, require mana for pets). The cap for these is much more likely to come into play.
Regenerations: not much need for Stamina regeneration - Many (if not most) take HP and/or mana Regen to their caps (which, the caps can increase as the pet slots improve - so always check back on the next training level).
Skills: Skill order means nothing. Using a power scroll will either cost 1 or 10 per point over 100, depending on the skill. MOST pets won't let you use a Parrying PS until Parry "uncloaks", which requires the pet reaching GM or better wrestling - but there are exceptions (some of my pets let me use Parry PS before the Parry value displayed, others did not). IF you plan to add a Parry PS, make sure to either save the points needed, or not do last slot training, until after Wrestling hits 100.
Note that unlike CC, the EC can display your pets' natural skill caps (not sure if that's native or from Pinco's UI), so you can decide whether or not to PS something (for example, as I had a pet that had a natural wrestling cap of 116.9, I chose to not waste a 120 Wrestling PS and its point cost)
