Sincerly I think that QII 11.0 >>> QII 10.x !
Qsys is a very nice system and I'm doing my new design using it a lot.
Qsys at the moment has 2 big advantage respect SOPC builder:
1- all communications are "packetized" and so you can achieve faster speed (very difficult with SOPC when you start to have some fast peripheral on the same bus - I had in past quite a bit of problems in order to let a DDR2 work with a Stratix III)
2- A slave that is accessed by 2+ different master will be seen by each master with a different base address (that can be the same, but CAN BE DIFFERENT - sopc cannot do this).
Moreover a lot of problem of QII 10.1 has been fixed (graphical entry expecially).
Told that I still prefer the interface of QII 9.1sp2 that except for Qsys imo is the best release ever, but unfortunatly there is a bug with Stratix IV gx with the Hard IP of PCIe (do not check some thing such as that the links to be used are only of GXB0 and others) and so I'll stuck to QII 11.0.
The byteblaster issue is a bit annoying but at the moment I've resolve it as suggested on the websites.
About nios, I've never used it before this version so I cannot comment.
Sincerly I love qII 9.1 sp2, I hated qII 10.x, whereas I like the qII 11.0 atm also if it's not perfect.