On the other hand, you can't have hybrid gas/electric with MT. It's kind of a bummer because I like responsiveness of manuals but the milage*power level is falling behind some automatics. Regenerative braking, continuous gear ratios, ultra-lean burn, and cylinder bypassing need to be coordinated with an AT. The decision was much more clear-cut a few years ago when you chose between a peppy 5-speed manual or a sluggish 3-speed automatic. Now cars like the Accord Hybrid make the decision tough.
If we get fuel cells in marketable condition there may not be multiple gears anymore. You'll just have a knob to select how much regenerative braking you want when you take your foot off the throttle. Crank up regenerative braking and you'd have lightning fast response to throttle changes.