Personal preferences vary so you're the one to make the decision. A lot of us prefer the manual shift over the automatic, but many others, as evinced by the fact that it's all but impossible to find a manufacturer selling a manual shift car these days.
If money is the driving point behind the decision, a shift kit is the right choice since you don't need the bellhousing, clutch, flywheel, transmission, clutch actuation system, pedal, etc.
Toploaders are expensive - in the same general range as a new T5z. The crossmember for the T5 isn't all that much ($270-ish). I didn't have to change the driveshaft when I went from a C4 to the T5, but others have had to. I don't know what differences in configuration would drive that change but some have had to have the driveshaft shortened. A good driveline shop can do that. If you go with the T5 there's also the choice of which clutch actuation system to use - Ford stock Z-bar, cable or hydraulic.