In the long run he was NEVER going to truly rule as part of the Empire, even if he benefited at first and became Dooku's apprentice, it would have still bitten him in the butt hard.
Outcomes:
Dooku would INSTANTLY have seen Krell for the slimy, overconfident, childish, power-hungry, deranged, impatient brute he was, deemed him unfit as a new apprentice and had him painfully murdered on the spot. After lecturing him about how out of his depth he was no less.
If Dooku had accepted him, Krell's insanity, hatred of clones and narcissistic attitude would have been a constant thorn in Sidious's master plan and the latter would have instantly had Krell killed himself. For an added bonus, Krell did not foresee that Dooku himself was not going to live to see the new order and had no idea who the REAL Sith Lord was.
Krell mistakenly believed the clones were feeble-minded creatures and thus had no idea that they'd been programmed with Order 66, thus they were actually the TRUE cause of the Jedi Order's destruction and he too would have been among the hundreds of casualties because he'd failed to see the actual outcome. Turncoat or not.
Had Krell lived to see the new order, again, his plan to be Dooku's apprentice would be naught, and there would already be the matter of Vader and Sidious, so he'd be stuck as an Inquisitor. If only because the Emperor would see some use in his brute strength, sadistic traits and battle strategies.
No doubt he'd despise this because he wanted as much power as possible and to be a simple dark-side soldier, answering to a Pau'an no less, would make him even angrier.
He would constantly upstage all the other inquisitors, try to take charge in every situation possible, cause as much needless bloodshed as possible for no reason when there was already a strategy thought of, try to cheat his way up in becoming Grand Inquisitor and his brutish, violent, power-hungry behaviour would mean constant arguing and fighting with all the other Inquisitors. He'd want it all to be about him and hog all of the spotlight for himself whenever the Inquisitors were supposed to be a team.
He'd probably be even more of a thorn in everyone's side then Reva the Third Sister. Before he'd know it, Vader and the Grand Inquisitor would lose their patience with his selfish, violent, unhinged, power-hungry ways and have him humiliated and executed.
No matter what, Krell was a complete butt-hole who put his pride, lust for power, sadism, violence, hatred of clones and selfish needs above all else, which prevented him from fully seeing the rise and outcome of the new order and this would have screwed him over big time no matter how far he would have gotten.
Heck, seeing Vader emotionally break, humiliate and near kill him in a "duel", like he did with Reva would have been INCREDIBLY satisfying!!!
