I have to admit, I have been designing my prints literally with "double standards". For fonts, I stuck to Helvetica because it's the MTA standard, but for colors, I tweaked them a little to make them my own: 

Part of this comes from the graphic design class I took with professor Gavin Cooper, where he told us how primary colors tend to remind people of corporate logos - primary red and yellow will remind people of a certain fast food chain, and primary green, a coffee shop. And so I tried to push the colors a little off the original MTA pantones.

I don't think I am the only one who thinks like this. For example, I do enjoy the colors of these prints found on the design boom shop, by SuperWarmRed:

On a side note, not until I made this comparison graphic did I realized the letters N, Q and R in MTA standard are black because they are against a yellow background - a relatively light color. But I decided to keep the ones on my prints white, sacrificing a little bit of legibility for consistency's sake.