Actually, it's been my experience with another small off-road vehicle (which shall remain nameless) that automatic trans versions actually have better acceleration and overall driveabilty than the manual trans version. There are several reasons for this:
1) Modern automatics (overdrive or not) that use lock-up torque converters can use a "looser" (higher stall speed) torque converter, since the stall speed is irrelavent once the TC is locked. The looser converter allows the engine to "jump" into it's powerband almost immediately.
2) As I pointed out in the earlier post, you don't need to let off of the throttle to shift. Since you need to shift twice with a 5 speed manual trans to get to 60 mph, and each shift will take at least one second, that's 2 seconds off of your 0-60 time with an automatic. (Any of you who are powershifting your AX-5s have transmissions that shift a helluva lot better than mine!) The full-throttle shifts are especially useful with a turbo, since the turbo stays spooled up; there's no blowoff pressure to slow down the turbine.
3) The torque multplication factor of the torque converter (typically 2:1 or better) gives you a REALLY low first gear. With the 700R4, the 3.06 first gear combined with the TC gives an effective ratio of 6.12!
While you might think of a 700R4 (usually associated with V-8 engines) as overkill for a 4 banger consider this: the version that fits the Jeep 2.5 was used behind a 120 HP, 2.8L engine in a 3200 lb. vehicle (80's Camaros and S-10s). The pumps on these transmissions (which are what makes automatics use more power than manuals) were sized for the smaller engine, and use less HP than their V-8 cousins. The clutches, drums and sprangs are the same as the V-8's though, which should make them damn near unbreakable behind the smaller engines.