Honestly, TR probably have stock as your best option most of the time. Burst fire pistols are extremely powerful especially in frantic CQC situations you usually pull your pistol in. If you can shell out some money or grind certs, the Commissioner + Knife combo is a tried and true method for taking down a guy from full health. It also works for the Crossbow and Repeater if you want, it's just that Commissioner will give you speed but also range.
Aside from that, I'm not a fan of the Emperor because it's basically the middle ground between the Repeater and the Commissioner, but it doesn't have either of the advantages leaving you with a subpar gun. Inquisitor is fun if you want to spam bullets everywhere. It's basically like having a secondary SMG if you spam it fast enough. Repeater just doesn't have enough ammo capacity to compete with it. The Amp is the literal SMG since it's a machine pistol. From what I've played with it, it's pretty shit so far. It just doesn't do enough damage to be worthwhile.
If you really like Stalker Cloaker, you're probably best off using Commissioner for the bodyshot + knife combo or the crossbow since it's silent. I would personally roll with the crossbow since if I'm running stalker, I'm going to be trying to lay down motion sensors, capping points as soon as people leave, and camping corners, and having only silent weapons just helps me remain undetected for longer.
But then again, this is coming from a guy who almost exclusively plays Engineer/Light Assault. As a side note, we really should organize a time for Planetside 2 so we can have a subSPUF squad. I'm pretty sure I still own the subSPUF outfit too.