Just to preface this: I'm no pro with a manual and did an auto-to-manual swap in Dec. last year in my 2K DX. I bought a JDM S8G gearbox because the price was low and the condition of the transmission was excellent. There are no mechanical issues with this transmission that I can detect. This is an oddball transmission in the US but is probably equivalent to that of EX with a very slightly different 5th gear.

That said, my only other experience with a MT was on a pickup truck, and by comparison, the first gear on this tranny is useless.

This thing in first just seems to make alot of noise while not moving the vehicle in any substantial way. I always start in second now which gets the vehicle up to speed quickly while avoiding pissed-off motorists behind me when I have to fiddle with first gear. Going from first to second just seems way too fast for this to be practical.

So -- is this a Honda thing, my driving or a completely *ss transmission? The second on the Honda transmission is almost like the first on the truck...

 

In general Hondas have relatively short 1st gears. Only a couple have a super low 1st (as used in diesel trucks).

All D series manuals use a 3.25 1st (some not sold in the US have a slightly longer 1st). Even with a 3.722 FD (some hydro transmissions) 1st gear isn't so short that it can just be skipped. You'll have better economy and longer clutch life if you use 1st gear. If something is actually wrong with the trans preventing 1st from functioning correctly you should have it repaired.