Don't know the exact reason, but a couple of guesses:

- A lot of the databases that airlines use tend to be on some old mainframes (black screen type systems) that might only be able to handle 3 or 4 letters and/or numbers. Very possible that it's a technical limitation
- Less confusion. For example, at Delta, the A319 fleet is N3xxNB, while the A320 fleet is N3xxNW or N3xxUS. The fleet numbers are 31xx for the 319s, 32xx for the 320s. Easier to remember that way than remember which last two letter clarification goes with each. As mergers have happened, you see a bit more of that type of overlapping since airlines aren't re-registering planes like they had done in some previous mergers. (Southwest is really the exception to this, as it's re-registered all the FL planes).