I'll give you my 2 cents, which won't amount to much since I have no clue what goes on. However....
I've religiously used TM from the day I bought my AXE. It's one of the coolest features and my mail reason for having the MKII and the XL+. It's helped me create so many sounds, I can't even begin to tell you. All of the above said, I'll give you my opinion.
I've had a few sounds with TM blocks in my arsenal for quite a few years. The only thing that has altered them is FW updates where the amps have changed. This nasal thing people are talking about....I've never experienced it OTHER THAN when I have used an amp that just doesn't work for a particular sound or when a monitor/cab may not reveal the source in a good way.
For example, the 5150 type amps aren't going to get an old Eddie sound using a TM. You're going to exploit the highs in that amp even more, and bring out an almost transistor, fake sound out of the amp. For certain sounds, you gotta choose an amp that has major tube characteristics. That means, more of a dark, warm, mid range type tone with a good saturation. Or, you could try a cab along with the TM....I have tried that with success with a few tones.
When I get people that hire me to create custom tones for them, the amp selection is as HUGE as having their DI signal to work with. I created a George Lynch tone for a guy where the amp we used, certainly wasn't one George would use and it was one I have never heard of. But for the song he was wanting me to nail, no other amp touched what this one did.
Those of you that have tried my VH patch and like it. That amp I used isn't too popular with most people that I read on here. BUT, that amp nailed pinch harms just like early Eddie, and has a nice break-up when coupled with a compressor. Anyone can get a similar tone when tone matching, but there are certain elements within an amp that you need to seriously consider when doing any type of tone copping.
The amp selection alone takes me about 2 hours + when I create custom tones for people. I literally go through every amp using various settings to see if it helps to pick up the artifacts, good and bad, just like the stuff I'm copping. You pick the wrong amp while tone matching, and you'll get a dick sandwich with extra veins. I'm dead serious. When I was choosing the VH amp while tone matching "Unchained", that nasal sound was very apparent in quite a few amps. But once you find the right one that just has the amp voicing and characteristics that you need in your tone, you just know it's right. There will be no nasal artifacts.
That said, there are only about 10-12 amps that I absolutely dislike in my AXE units. The rest are all killer and you should be able to tone match anything with them and get close. But to really nail a TM, you have to pick the right amp and really listen to what you are copping. Listen to every aspect of the sound, etch it in your head and then proceed with your amp selection.
The tone match block is only copping what you put into it. Next, I sincerely believe your listening environment makes a huge difference like someone already mentioned. Quick example, I had a client come here for me to do custom presets. He brought his matrix cab and power amp. He wanted his own version of an Eddie sound using his signal.
What we got was a nasal, horrible sound that sounded nothing like Eddie....or so we thought. Then we played Eddie through his cab and it sounded the same. Nasal, and nothing like Eddie at all. So if I were tone matching through his rig, I'd be pissing in the wind because Eddie sounded nothing like Eddie through that cab from the start.
If your sound source doesn't sound good coming through your cab that you are going to cop, your final outcome should sound the same....unfortunately. I use studio monitors here that are calibrated and my room is tuned. When I play something here, it sounds like it should sound. Now, for live tone creation, I can't rely as heavily on my studio rig. I literally have to tweak once it comes through my cab.
Now this is where things get strange. When I pipe Eddie through my greeback cab, it sounds like Eddie in my room. This is what I tweaked my live tone against. So in certain situations, what you hear is definitely what you are stuck with. Sometimes good, sometimes bad. In the case of the client that came to my studio, there was no way I could create a tone from his cab and make it something I would enjoy. That's not a knock on the matrix, that is just to say....guitar sounds from national acts sometimes don't sound very good coming out of that. It's like trying to mix in a room that isn't tuned with uncalibrated monitors, and then you go out to your car to listen to what you did.
You find that in your car, you hear things differently. So you take notes and go back to your studio, and try to mix something you can't hear, follow me? That's how I felt with the Matrix monitor. What came out of it from the source wasn't something I liked, and just about all of us like EVH's sound in "Unchained".
Anyway, those are my thoughts and experience on the whole TM thing. It's far from useless on my end and has made a world of difference for the better in my realm. I can totally understand where it may not be for everyone, but definitely keep some of the stuff I've said here in mind when doing it. It may just help you.
-Danny