I think this is really odd, since the MAME devs in almost every other part of the emulation prioritize correct emulation before gameplay. Why did they choose to do like this for the shifters?
It came about because for keyboard and gamepad users (including those who were writing the drivers), it was a PITA to hold down a button to stay in gear.
I can't code, but Dmod made a diff file for an older version (127 IIRC) and I've been able to manually copy and paste the changes to newer versions before compiling. Of course, this just gets rid of the PORT_TOGGLE so the game behaves as it would originally. That's good, but it doesn't add any flexibility for people with other types of shifters like the sequential shifters that return to center. I never played the old sprite based games before fixing the shifter. Now I like them as much as the newer 3D games.
baritonomarchetto has a working solution in RacerMAME that allows you to use the original, toggle, or even sequential shifter.
It's based on MAME v.106 though, so I don't know how well it translates to current builds.
I've started threads about it hoping someone who can help would take an interest in the issue, but they've all gone nowhere.
We can talk about it all day, but when it comes down to it, we're mostly end users, tinkerers and woodworkers on this board.
Until someone knowledgable enough to submit code that would be accepted into the main build takes an interest in it, it's not going to be done.

EDIT: And if anyone reading this happens to take an interest in it, here is a spreadsheet of the affected drivers.
https://docs.google.com/spreadsheet/ccc?key=0ArE1chsgHXQodDd2ckdjLVY3Ujlad2tZWUpteDNtcXc&authkey=CIrIhMwE&hl=en&authkey=CIrIhMwE#gid=0 Click the shifter hack column and read the full description at the top of the spreadsheet.
Only updated as of v.141 RIP MAWS
PORT_TOGGLE has been added to two or three drivers since then. I can find the info if needed.