So, to be fair, let's start out by saying that while you're asking about version control, PBNative is source control. If you compare something that is intended to have more features than just keep two developers from editing the same piece of source, then yes, PBNative will suck. The Madone SL may be an incredible bicycle, but if you're trying to take a couple of laps around an Indy track, it will suck.
"Best" is a pretty subjective word. There are lots of features available in version control and configuration management tools. You can get tons of features, but you'll pay through the nose. StarTeam has some nice features like being able to trace a client change request or bug report all the way through to the changed code, and being able to link in a customized diff tool (which is particularly useful in PB). Then again, if cost is your key criteria rather than features, there are lots of free options that will get the job done. As long as the tool supports the Microsoft SCC interface, you should be OK.
There is a relatively active NNTP newsgroup that focuses on source control with PowerBuilder, which you can also access via the web. You can probably find some already-posted opinions there.