Undead revisited and the bestiary, iirc in the bestiary it tells you that the creature you turn loses a lot but keeps natural abilities like reach for a "faceless stalker"
From the title we can assume Aikidoka is talking specifically about skeletal champions, which do keep their class levels
Aikidoka:
From a quick scan of the template on the SRD, there wouldn't be any reason why wizards and sorcerors would lose their spells, so you are fine there.
In terms of a cleric, purely RAW nothing is stopping it from the champion praying to its original god and recieving spells. However, if that god was a good god, the new skeletal cleric will probably not be getting any spells from those prayers.
There's no specific rules for changing gods, but it is perfectly believable that the new skeletal cleric could worship a new (darker) god and change domains to ones better suitied to its new predicament. Ultimate campaign retraining rules includes a way of retraining domains if you want something more concrete.
only if they want to follow a new god. turning people into skeletal champions does not means they lose there memories so a undead cleric of iomadea may seek to end its own life yours or to find someone that will do it for him. Best way I found around it when I played one was Command undead which can be difficult unless you boost your turn DC. Once in control useThrenodic spell to place a geas-quest on them with the stating they are to serve you to the best of their ability nor in any way that will impede my goals willfully short term or long term. My direct commands being the only thing that trumps that. That should cover all bases if they get out of line like refusing to do something dangerous you can always command them to fail their next will save and Command undead them to gain complete control again
only if they want to follow a new god. turning people into skeletal champions does not means they lose there memories so a undead cleric of iomadea may seek to end its own life yours or to find someone that will do it for him.
Skeletal champion changes their alignment to Evil, so they probably won't have the same outlook as before.
But yes, controlling them in some fashion is a good idea. Regardless of their new opinion on existence it is unlikely to align with yours perfectly. I like your threnodic geas idea! Unfortunately RAW you cannot do this as geas may only target living creatures (threnodic spell doesn't get around this, it only bypasses the immunity to mind-affecting). It's a fair houserule though.
Any DM worth his salt would leap at the opportunity to explore the moral dilemma of being brought back as an undead. Hopefully you have some fun with this, Aiki!
journeyquest did this...it was hilarious