So Trump would file a suit in federal court claiming that NY has failed to follow his pardon. He becomes the litigant, not to defend Bannon, but to defend his claimed right to pardon whomever his wishes.

Should the courts toss out the case? Of course they should - and very well might. (A bit of venue shopping might help. Don't file in the SDNY for one.) But that still leads to appeals and eventually to the USSC.

He can claim whatever he wants, but the President wouldn't have any standing in such a suit. That's not how the courts actually function. If the parties to a prosecution have a legal right that isn't being observed in the lower court, then they parties can file appeals. But the President cannot.

Nor would any appellate proceedings in that third party case slow down the actual prosecution unless Trump actually won. Unlike the immunity challenges, which allowed for interlocutory appeals (basically appeals before final judgment) and a stay pending those appeals, this would be an independent collateral attack on the proceedings. IOW, Trump can't slow down the Bannon prosecution simply by filing the challenge - he has to win a motion for an injunction.

It's just not a plausible scenario - even stipulating that the SCOTUS is very deferential to Presidential power, this is an instance where the scope of that power is so clearly limited to federal matters and where the President is so clearly not a party to the dispute, he's not going to be able to affect things. Bannon can raise the issue, but not Trump.