Shadow jaunt is distinctly limited versus other teleportation effects:
You must have line of sight and line of effect to your destination.
Most teleportation effects require neither. That means that darkness, clouds, fogs, mist, to say nothing of walls and other barriers, all block shadow jaunt. Shadow jaunt is an effective way to climb cliffs and/or cross chasms, provided that neither is greater than 50 feet, but at this same level things like spider climb can also do that.
The fact that shadow jaunt can be used every other round very rarely, if ever, actually matters. In combat, using up three rounds jaunting, recovering, and jaunting means the fight’s already over by the time you finish. Out of combat, it’s probably faster than just climbing but unless the party faces a series of chasms or cliffs, you’ll probably only use it a few times. And if the party is facing a series of chasms and/or cliffs, hey, abilities are allowed to shine every now and then.
Also, keep in mind that 3rd level is when 2nd-level spells and powers come online. Spider climb can be used for a lot of the things that shadow jaunt can, albeit slower (but without the 50-foot limitation). Dimension hop is actually a 1st-level teleport, though it is limited to only 10 feet (20 feet if you spend 3 power points on it, as if it were a 2nd-level power). For that matter, at 3rd level, anklets of translocation are affordable, and those grant a swift-action 10-foot teleport 2/day. These things are all comparable to shadow jaunt—shadow jaunt is a bit longer, and can be used more often, but these are “real” teleport effects and therefore able to bypass a lot more obstacles than shadow jaunt can.
And on top of those, the conjurer’s abrupt jaunt from Player’s Handbook II is a (Int bonus)/day immediate-action 10-ft teleport. That blows shadow jaunt out of the water. That, in reality, is overpowered.
So shadow jaunt is good—even very good. But it is not overpowered in the sense that it completely outshines comparable options at the same level. It’s just competitive with them—which it should be.
To my mind, the only really weird thing about shadow jaunt is that it’s Extraordinary, not Supernatural. Commonly house-ruled, though I think the intent is that the “teleportation” is actually a combination of incredible speed, stealth, and acrobatics (hence not actually traveling through walls), and that’s why it’s Extraordinary. Not really that much of a balance concern, though it certainly may surprise a beholder!