My 03 999 is considerably smoother than my 998S, as you described. The 998S has Termi, the 999 does not. The difference in how the bikes feel has everything to do with rider/bike relationship and geometry. You are perched on the 998 and feel more like you are in the cockpit on the 999 bikes.
Perhaps tire pressure was also a bit low on the Matrix as compared to the 999 you rode.
I much prefer the 998 to the 999 as I feel like Iím more part of the bike, if you know what I mean. Iím not a big guy, but an old guy 57, 165lbs, 5,11.
Also, while they both have the same lump, the 998 sounds bloody wicked with the pipes. Raw, like you described. IMO the 998 has a more race bike feel, the 999 more refined ride.
749 is completely different bike Ė very quick to spool up and feels much lighter, but does not have the grunt of larger engine. Itís a fun bike, buy no kick ass power delivery as you described for the 998. I prefer to ride my 749S, with full Termi, over my 03 999.
If I could only have one of these three it would be hands down the 998S.