Always felt a near ideal general purpose MTB or MGB (for either side of the war) would have looked a lot like an E-Boat / S100 -- for the Atlantic they were able to operate at high speed in sea states the PT boats couldn't get on plane, and in the Pacific they had far greater range and endurance than the PT boats and would have been right at home among the islands in Guadalcanal
Size vs visibility was an issue as was engine power, the larger the boat, the slower and more visible it's going to be and as the size groe, you end up with a corvette (witness the evolution of the Israeli missile boats, for example). In WW2 the S-boats were larger than the other nations boats but their successes came mainly by the unpreparedness and/or lack of training of their enemies (ie Exercise Tiger - where the escorts were pulled out of Atlantic escort duty).
By 1944 the counter was the aircraft and the operations were restricted to night minelaying mainly.
Also there was overclaiming and ships that grew in the mind of the S-boats commanders from 100s grt to 1000s grt, so they were useful to have but not very cost effective, so resources would have been better spent on more R boats.
No argument here on the overclaiming, it does happen, and of course how they're employed has more to do with their success or failures than anything else.
Paper top speed and actual top speed will of course differ, but everything I've been able to find suggested that the E-Boats were generally faster and a more stable gun / torpedo platform than the 80' Elcos (both laden with ordnance) in all but the glassiest of seas -- a lot of the planing hull type designs of the MTBs tended to beat themselves apart at high speeds in open ocean testing. The E-Boats also had Lürssen effect fins (not quite hydrofoils, but it lifted the ass and gave you an on plane like effect while reducing the drag and wake) discovered by happenstance.
Without seeing a head to head, I suspect the MTBs would accelerate faster and have a tighter turning circle though just based on it's design characteristics, which would certainly have its merits.
At night from the frontal aspects the size is so close as to be a wash IMO, both are about as low to the water as is practical, and in either case the wake would be the giveaway before anything else. Night operations are really the only way to go with either type if you're dealing with anything that can shoot back. One of the reasons I do prefer the S100 is it's large enough to combine the usefulness of MTBs with MGBs without giving up anything that would hinder it's ability to do either job. It is a larger boat though so the most apt question would be: could smaller manufacturers that built the wooden MTBs also build something larger like an S-Boat, and would build something larger like the S-Boat take work away from even bigger, more useful ships?