I'm going to give you a few more subtle differences between the units that maybe you didn't detect while reading the specs.

The MFII, as the UFX and UCX, can be used on a desktop computer (via the PCIe or the PCI card) and on a laptop, via the XpressCard. Both work beautifully (I own both solutions). But remember that it's increasingly difficult to find notebooks with xpresscard slots today. On the other hand, you'll always find a USB slot on any computer. RME implementation of the data transfer through USB bus is of a very high quality, so don't think that getting a PCI or PCIe implementation will have less problems. Maybe that was true 5 - 8 years ago, but not today.

Second, and very important, the MFII cannot be used as a stand alone unit, while UFX and UCX can. That means that UFX and UCX can be effectively used as _external converters_. You can store routings from analog inputs to the ADATs; or they can be used as a matrix router. The MFII can only work while connected to the PCI/PCIe card.

Third, the MFII can only make use of the old Totalmix. There are certain features missing there, in comparison to the UFX and UCX. Also, no internal FX on the old MFII.

All these products have WC input and output, so you won't have problems synchronizing the units to any kind of external converter connected thru ADAT. Obviously, you can also use the clock signal comming thru the ADAT input as master clock. Or you can use the units as master clock for the external converters. If you've never used a RME unit before, you don't have an idea yet of the incredible flexibility they give you.

You're welcome.

Correct. Remember that you only have 1 ADAT in, so you cannot use 96 KHz SMUX (once more, only needed for the golden ears
Can't say anything about prices right now. But the breakoutbox + PCIe or XpressCard should be near 750 € (at least in Europe)... That's almost the same as a FF400.
About quality ... New converters of course are better. Not only in the sense of a slightly better SNR and "less" THD, but there are a few subtle things that can be important for you. One, for example, is latency. New DACs and ADCs usually are a little bit faster than the old ones. Also, of course, hi-gain pre-amps on the UFX/UCX are just gorgeous, and are going to have lower noise figures and better than the older ones on the FF400/FF800, and this is really noticiable, specially at high gains.

[q]UCX:
-    Cheapest USB solutions for 8 analog input (or 16 analog input using ADI-8)
[/q]
Not sure cheapest. I think a UC is a little bit cheaper, isn't it? As with the MFII, no SMUX (only 1 ADAT)

[q]
UFX:
-    Cheapest USB solutions if 12 analog inputs is enough. The price per input seems to be cheaper than a UCX with a ADI-8.[/q]
The UFX is such a beast that referring only to its 12 analog inputs is almost a crime

[q]That the unit can work standalone is for me not very important. About PCIe, i thought that this is still the most stable connection nowadays. I realize that it might be a problem over 5 years. But firewire is already abandoned on some of the newer motherboards. From what I read regarding the UFX is that USB is less stable and has more problems than the firewire connection.[/q]
If you've taken a look at the forum, then I cannot add more. Yes, PCIe is yet the more stable solution. But you cannot use your unit live unless you invest on the XpressCard.

[q]If this is the case the MF2 looks like the best option. However, on the Internet I read from a lot of people, who updated from the FF800 to the UFX, claiming that the sound quality noticeable improved.[/q]
Sorry, but I don't believe it. The converters are better for sure, on paper and while using our marvellous Teks or Agilent oscilloscopes and measurement tools, but ... not when using your ears. The fact that some people actually hear a difference is a problem with our brain . http://youtu.be/BYTlN6wjcvQ

Of course, if you intend to use your unit not for musical purposes but as a data adquisition system, you could tell the difference .