non-intelligent undead cannot take feats. Or skills for that matter. They need a minimum intelligence of 1. (Vermin are the same in this regard)
Generally speaking anything that will grant the undead intelligence will also probably break the 'companion bond' as companions are strictly ruled and quantified to maintain balance. Look at animal companions and the spell awaken. The spell states that the animal the spell is cast on cannot serve as a companion.
If you want an aware undead 'companion' your best bet is going to be something along the lines of create undead once you get high enough level. Create an intelligent undead being and every level you advance, create another creature more powerful as well. Either that or leadership.
non intelligent undead can't take class levels because they are dumb
Quick aside: they're not dumb. They're mindless. Zombies for instance can understand spoken commands just fine, unlike creatures with a 1 or 2 intelligence.
Does that mean undead can take class levels?The "crunch" doesn't prohibit it, but the "fluff" does. They're mindless, uninterested in anything but destroying life.
How do you add templates to a creature after it has been created?
Magic. (Usually, you can't. But some specific spells change the nature of a creature.)
the two lowest CR undead I can think of that can have class levels would be the skeleton champion (already mentioned) and the juju zombie.
http://www.d20srd.org/srd/variant/classes/specialistWizardVariants.htm#necr %20omancerVariants
Yea i was using this 3.5 variant. I realiswe this is kind of homebrewing, but i was wondering if there are any pathfinder or 3.5 rules for stuff like this. The skeleton template rules are not very clear, for example it only says that feats are lost, not that you can't gain them as you increase HD, while for skills it exp;lictly says that you dont gain any skill ranks.
I also don't get how creatures are supposed to gain templates (other than the DM applying it to creatures he creates). I'm guessing there are no rules for when a creature can gain templates? Like when can you create a skeleton champion or warrior rather than just a normal skeleton?
Typically you don't 'gain' HD as a skeleton or zombie or etc. What they are created with is what they have, it doesn't 'get better' or advance with time.
Templates for undead are typically applied at creation, there are very few templates that are applied on the fly just because they can be.
The only rules I know of regarding advancing a creature who is permanently 'attached' to a PC are familiars, animal/companion type bonds (various classes/PrCs) and leadership. What you are looking at doing falls under the leadership 'umbrella' from what your questions have been so far. It would allow for you to have an intelligent companion who would have the option of gaining class levels as you level up. There are no rules for leveling up intelligent undead minions (skeletal champion, juju zombie, etc.) outside of the loose rules of the feat. Just rules for creating them, so RAW they stay the way they are created.
Why can normal creatures gain HD but not undead?
Only skeletons and zombies have this restriction; it's specific to these types of undead, not undead as a whole.
The "skeleton champion" is what you'd use if you wanted to create a skeleton that can level up.
Why can normal creatures gain HD but not undead?
Besides the fact that it is a minion npc and doesn't gain XP unless the GM says it can? Again Leadership is the only rule I can point to that gives a PC controlled NPC actual advancement. Anything else is 'as created' and would only advance if the GM says it does. Undead minions that are created by a character do not get a share of the XP for an encounter, the party isn't considered one or more larger because of the minion(s). The PC party isn't 'docked' XP for having the minion with it.
Now if your question is why a creature cannot advance in general, mindless creatures are generally limited in what they can do (as mentioned in the template, not gaining skill ranks etc.)
Why can normal creatures gain HD but not undead?
Besides the fact that it is a minion npc and doesn't gain XP unless the GM says it can? Again Leadership is the only rule I can point to that gives a PC controlled NPC actual advancement (beyond familiar/companion bonds). Anything else is 'as created' and would only advance if the GM says it does. Undead minions that are created by a character do not get a share of the XP for an encounter, the party isn't considered one or more larger because of the minion(s). The PC party isn't 'docked' XP for having the minion with it.
Now if your question is why a creature cannot advance in general, mindless creatures are generally limited in what they can do (as mentioned in the template, not gaining skill ranks etc.)