What's interesting is that the apps that don't work often does this for other reasons than the CPU. I don't know how it's like in the Amiga world, but in the Atari world there's a lot of applications that make assumptions about screen layout, sound hardware, RAM etc and when you create a new computer it's hard to get these things perfectly backwards compatible. I have a Falcon, a Falcon with a 040 accelerator and a Milan060 (Atari clone) and the problem is always the same - the previous generation of software doesn't run or run with problems.
The Amiga has a similar problem. Most application programs, even from AmigaOS 1.x, run fine on a 68060. Games from that time period are a different story. Many do not work. The most common "CPU" problems are much bigger caches and trapping of instructions without the (software) 68060.library installed. The 68060.library installed from flash for bootable floppies and CD-ROMs takes care of the latter but is not common except for 1 68060 accelerator and the Natami 060. The 68060 allows 1/2 the caches to be turned on but that's still too much for many old games. Compatibility of the 68060 with 68020+ is excellent overall. Other misc problems with old software is more common than CPU problems. I think there are fewer timing problems on the Amiga though. There were a few early games that ran way too fast on an accelerated Amiga but that is rarely a problem since AmigaOS 2.x days. C= was telling developers what not to do for future compatibility at that time. I guess some listened. We do have fixed/patched/WHDload games that solve many of the problems with old games.
I would love to have a fast machine with a "real" 060. But currently there it no such thing. Even when running 68k code the Firebee is faster than the fastest 060 (which I think is a Falcon with a 100Mhz CT60). And the 060 is not without issues either.
I wouldn't call the 68060 slow. The v4e ColdFire out clocks the 68060 by enough that it's going to be faster with ColdFire code but the 68060 can still hang with 68k code. The 68060 also benefits a lot with 68060 optimized code. Several instructions are faster per clock on the 68060 not even considering that it can execute 2 or more at a time much of the time. The ColdFire does add instruction combining/fusion and a link stack (for fast bsr/rts) which helps with 68k code. The new ColdFire instructions are useful but don't help with 68k code. The missing instructions and addressing modes are a big handicap with 68k. I would take a Natami 060 (or CT60 if I was into Atari) with 68060@100MHz any day over the CF v4e. I have a CSMK3@75MHz with 50ns SIMMs and 30MB/s sustained HD speed. The 68060 is no slouch and really has very few issues.
Maybe it's possible to implement a softcore "060" that outperforms a V4E. But currently that seems to be difficult. Also, the V4E does all sorts of stuff that must be replaced if you go for a softcore. E.g. it has a DRAM-controller, ethernet, PCI-controller...
The ColdFire's main advantages are built in hardware support and a cheap price.
The CPU is only a part of the equation. You need to support all the other legacy hardware too, and maybe even a cycle-exact 68k. If you replace the 68k on a Atari ST or Amiga 500 with a 060 you will still have compatibility problems.
Nothing faster is going to be cycle-exact. UAE Amiga users don't even use cycle exact. The fpga processors will not be cycle exact. We don't need cycle exact. It really only applies to 1 particular processor and <1% of Amiga software needs it.
The Coldfire is powerful enough to emulate a 68k in software when you need it. Combine that with implementation of legacy chips in the FPGA and you have a machine that can both be more powerful than a 060/softcore-based AND more compatible.
Well, that depends. There are very fast fpgas that could contain a CPU faster than the v4e ColdFire. They are very expensive now but dropping in price quickly. The CF series doesn't look like it's going anywhere. The v5 CF is available in large quantities with whatever bolt-ons are wanted but it's not being marketed. It looks to me like the end of the line as far as CF improving. We can probably leave away the pure 68k software emulation compatibility as the 68060 can do that nearly as well as the CF and UAE on a high end modern processor kicks everybody's ars. Let's compare the v4e CF to the fpga Cyclone IV Apollo core as will be used in the Natami. The CF solution is faster if trapping can be kept to a minimum and much cheaper. The Apollo core will probably be a little faster than the 68060 but has the potential to be much more compatible. It will have bus snooping of the caches for self modifying code and any missing instructions or addressing modes will not be a problem. It looks like the CF has the advantage early on but it should narrow quickly as fpgas become cheaper. A chip could be burnt that includes the fpga CPU, the custom Amiga chips, a 3D core, etc. that would boost the speed to CF v4e speed or above. The price would be expensive unless a large quantity was created. The Apollo core could be used for an Atari project as well. We could go in together to burn an Apollo only CPU or perhaps a chip with Apollo core and custom chips for Amiga and Atari. An fpga solution opens up a lot of possibilities. The 68k softcore was separated from the main Natami project to appeal to more potential customers including the Atari crowd. Here is some preliminary specs on the Apollo soft core:
http://www.apollo-core.com/
Don't get me wrong, the Firebee is not perfect. Far from it. Some bad decisions has been made that unfortunately keeps it from being as backwards compatible as it could have been. But the CPU is not the problem.
Some poor decisions based on marketing were made by the ColdFire designers to remove compatibility with the 68k. The ColdFire is a low end cost reduced 68k processor geared toward embedded systems. Many of the powerful advantages of the 68060 were lost. Several of the CF instruction additions do enhance the 68k in both power and code density and should be included in the Apollo soft core. I hope you pay attention to the Apollo project as it evolves. Even if the next generation Atari crowd stays with the CF CPU, we will have more in common. Not only am I involved with the Apollo project, but I have worked with Frank Wille to add CF optimizations for vasm (improves vbcc code also). It would be nice if some of you Atari CF guys could do some testing

. We need better compilers for both projects and we can work together to enhance them. The latest version of the vasm assembler with the most CF enhancements has to be compiled with vbcc. The compiling instructions and source can be found here:
http://sun.hasenbraten.de/vasm/After compiling a new version of vasm, it can be placed in the vbcc:bin directory where it will then be used by vbbc. Watch those executable sizes shrink

. Contact Frank if you have any problems as he has provided great support including for Atari.