Hopefully it's Paul writing it.
Paul Dini is the only man for the job.
To my knowledge, he created Terry McGinnis. He's also one of the most solid Batman writers of the last ten years. As for an artist, I'm not really sure who I'd want. The only people I definitely wouldn't want to see as the artists are Bruce Timm (purely because we've already seen his interpretation of the character loads of times) and Ed McGuinness (purely because he is crap).
Also, I would suggest that this be independent of the animated series' continuity.
I'm pretty sure Terry appeared as a cameo in Loeb and Ed's Batman/Superman run.
If Paul Dini was in charge I would like it to be semi cannon.
Starting in June, BATMAN BEYOND — a six-issue mini-series from writer Adam Beechen (who’s no stranger to animated characters, having worked on The Batman series a few years back) and artist Ryan Benjamin — will pit the future Dark Knight against his own past, as a dangerous force has begun to target Bruce Wayne’s old foes. Can Wayne’s past put Terry’s future in danger?
“The dark future of the legendary animated series comes to the DCU in a six-issue miniseries, as Terry McGinniss, Bruce Wayne’s young successor as Batman, faces his deadliest foe yet — a mystery murderer from the Dark Knight’s past! Old faces return, new allies and enemies step into the light, and the partnership between Terry and Bruce — not to mention Terry and Bruce themselves — might not survive!”