When you shift into 3rd, there are more moving parts than your 1-2 shift, or your 3-4 shift.

In your 2-3 shift, you have to move the 1-2 synchro from 2nd gear to neutral, and the 3-4 synchro from neutral to 3rd gear. You're moving 2 synchronizer sleeves at the same time, so it's normal to feel the 2-3 (and 4-5) shift a little more than the rest. It should by no means be excessive, but a little louder/notchier/stiffer is to be expected.

New MTF wouldn't hurt.

 

This is your transmission:

|1|[=]|2| = |3|[=]|4| = |5|[=]|6|


|1| is the gear

[=] is the synchronizer

The synchronizer hub is fixed to the shaft, and it has a synchronizer sleeve that slides over it; it's grooved to accept the shift fork. To engage a gear, the shift fork pushes the synchronizer sleeve onto the desired gear, and locks the gear to the synchronizer, thus locking the gear to the shaft. Then, power flows from your input shaft, through the counter shaft, and then to the output shaft and the driveshaft.

Anyway, if you look at the diagram, gears 1/2 and 3/4 and 5/6 have their own synchro. If you think about it, when shifting from 1-2 you only use the 1-2 synchro. But when shifting from 2-3 you use the 1-2 and 3-4 synchro: Disengage 1-2 synchro and engage 3-4 synchro.