I also have an X5000 and I don't regret it. Bought the motherboard from AmigaKit UK and built my own machine, which I found quite rewarding.
Altivec would speed up certain mathematical functions, such as video encoding (which I do a bit of). For example, the SAM has a higher clock speed than my A1XE, but using FFMpeg compiled for Altivec on my A1 actually outperforms the SAM. I don't have an X1000 to speed test, but I wouldn't be surprised if the same held true for the X1000 vs X5000.
As I migrated software from my A1 to my X5000, I had to be careful to not use the Altivec versions I previously used.
It's a shame to lose Altivec, but the P5020 is pretty darn fast in its own right.
I have not had any major issues with my soundcard, although I do have quite a low end PCIe unit that only cost $NZ15 and performance matches price.
I wish OS4 had a better TCP/IP stack, but that affects all NG Amiga users, whether you're on a MicroA1 or a X5000/40. Had no problems with my peripherals. Mouse works (cheap Zalman model), keyboard works (not-so-cheap custom keyboard), printer works (with the venerable TurboPrint). Had a few issues with graphics cards to start off with, and I have no idea how I solved them, but if you buy a complete machine from a vendor you shouldn't have that worry.
The only outstanding problem I have is that I am unable to play or rip commercial DVDs. I can't figure out why. I don't know if I'm missing some software, or because the p5020sata.device hasn't been finalised yet (as alluded to above).