Well, since the TAS universe has it pretty set in stone that Barbara never becomes Oracle, Cassandra Cain doesn't exist as Batgirl, Azreal/Jean Paul Valley isn't apart of the continuity, and Huntress is really more of a side vigilante, I'd have to agree that an early days Batman: TAS Prequel type of series would be the best way to go, since they can't really introduce many new characters into Batman's current timeline without ****ing up the Batman Beyond/Future DCAU continuity.
Basically, I'd have him take on Sal Valestra's mob after Andrea leaves Gotham and he becomes Batman. This leads to his fight with Jack Napier, who'd become The Joker by the end of the first episode, but doesn't appear as the full-on Joker until later.
Since alot of Batman's rogues gallery really didn't meet him until TAS, which is apparentally quite a few years down the line from MTOP, they'd need to use one time villains that never made it into the DCAU series, like Dr. Death, The Monk, Nocturna, Black Mask, Ratcatcher, and others, so as to explain that they never came back, thus why they were never mentioned in Beyond/TNA/JLU.
Batman's allies could also be spotlighted in certain stories, such as how Leslie found out his secret, and what it took for him to recruit Gordon as an ally. Plus, we could see Batman's first attempts at different Batmobiles (Pre-"The Mechanic") and vehicles/weapons.
Of course he'd end up battling The Joker and The Penguin, but I think that's really it as far as major criminals that Batman had encountered before the TAS timeline.