Max datarate for FF is 1Mb/s and UDB implementation up to 8Mb/s.
The configuration differs a little bit. In a PSoC5 you'll find up to 24 UDBs that can be used for a lot of communication interfaces, while the FFs are more restricted.
I generally use the FFs first, so when I run out of those I can use UDBs.
There has been no rumor yet to abandon the PSoC5 line. The now upcoming PSoC6 could be a replacement but has more facilities and is of course more expensive.