If the maximum you can level up your pistol is level 2, then it is intended that the pistol is your secondary weapon. Thus it follows that your primary weapon will always outclass your side-arm. The clone pistol is in no way, shape or form, a substitute for your rifle. The clone rifle is the only weapon you can get. As for the debate around a normal pistol and a clone pistol: the clone pistol offers you the ability to bounce shot. I've not noticed a RoF discrepancy, but it's both meaningless and a (more than) fair trade-off when you consider bounce shots open up the ability to;
1) kill Sith that are blocking you face-on
2) kill low HP targets fleeing to cover
3) bounce-shot ruptor/projectile snipers from BEHIND cover
4) have a zero-risk spot checking tool
If the dev. team can confirm there is a difference between the rate of fire for the two pistols that would be great, because I've not really noticed a difference. Also on a side note, could the dev. team publish EVERYTHING regarding the numbers of the game? Maybe in the library, or a more completed spreadsheet that Mace had uploaded (I think?).
Comparing T-21 level 1 to clonerifle 3 is also a rather strange thing to do, because of the huge tier difference. You invest about 45 points for a CR3, it stands to reason that of course it will be better. Although, I do think I understand what you're trying to get at, in that you're using it as a counter-point to a high-damage, low RoF weapon being outclassed by a low-damage, high RoF weapon. I'm sure you understand that different guns function differently in different environments. Take for example any of the known EU BH players who are exceptionally good with the disruptor; qwerty and Ajua are probably the two that spring to mind. If I were to take a CR3, it would not matter how good my aim was, they would almost always win if we were to fight in DotF main corridor. From that, should I infer that ruptor is overpowered, or requires little skill? Of course not. Change the scenario, and put the fight at t-junc with a BH scoped in a typical position where the angle for him to shoot is not so acute. Not to undermine either player, but I think they would be hard pressed to fight back when at that range it is so easy to pot-shot and bait the snipe. After which, they're dead (provided you can aim).
The T-21 primary shot isn't supposed to be the main mode of the gun, it's your high-damaging alt fire that has a ridiculously low time-to-kill. The primary shot is incredibly strong in certain contexts, and it's a mode more suitable for long range insta-gibs. It's an irrational thing to do, engaging a CR3 with a primary shot and expecting to win, all the more so to engage the CR3 at close range where it dominates most other weaponary. If you're pushed up by a CR3 user, and you can only engage them where they are at their strongest, then it's more likely a team related issue if no one is stopping their advance.
I don't think there's particularly any grounds to nerf something when it's used in it's best situation, and I'm not saying that clones are easy to kill either. I think stamina 2 clone is the real cancer, but we must have the humility to admit that we misplayed.
It's how hard or how easy it is to do that is ever the question.