I think both will likely be around for quite a while yet. Especially given the recent influx of bulbs from China and other countries.

Recently I'd hacked apart a Coralife 4x65w fixture to retrofit it into my canopy, they used the straight pin arrangement, but the repalcement bulbs I wanted were in the sqaure configuration, (and half the price) a simple fix. Replacing the endcaps for cheap was easy, took all of 5 mins to replace with nothing more than a jewelers type screw driver to do all 4 once I sorted out the wiring. (For future reference It's posted in the DIY forum, I'll be adding some more wiring schematics to it soon as well).

For this reason I would not worry too much over the pin configuration if you are able to get the fixture or retros in the bulb types and spectrums you want now, changing your mind later is almost always inevitable.... even if it takes changing the endcaps to get what you want.