Wow, I never knew about those bugs. That's probably because I haven't played Duke that much - just ran through it once, but didn't bother to check all the intricacies the game had to offer. I also used the same behaviors like yours, running jumping into pools and emerging to the surface before approaching a shore - the former one because it was cool to do and the latter to see any danger from distance instead of jumping out of the water only to end up right in front of a shotgun pig. I wasn't aware those saved me from game crashes as well :D
The thing that used to get me with any maps that I made, and many of the maps I downloaded, was the flakiness of the 3D water teleport effect. Even if you had copy/pasted the source and destination sectors as exactly as possible, you could still end up with a slight mis-match by the time you came to play the game. So, when you came to teleport, you might get teleported to a location that had you slightly, and I mean ever so slightly into the void - like the very edge of the player actor clipping into the void by less than a pixel (or so it seemed). The engine was so sensitive that this would be enough to crash you back to DOS, leaving the screen mode in some big, ugly graphicy mode.
When playing a map in build, I just got into the habit of taking a running jump into any pools of water to ensure that I wasn't teleporting near the edge. That was usually enough to avoid the problem. Of course, surfacing (teleporting out of the water) was trickier but surfacing away from the edge and then moving to the the edge in order to leave the water would usually do it (unless you accidentally slipped below the surface again).
That's why I like Carmack's engines. He always put stability before new features and implemented them only when stability was assured.
Personally, I'd choose a stable engine with fewer features over one with more possibilities but with some critical flaws. However, Duke pushed FPS genre forward with those features and it definitely was an evolution which inspired other programmers. I prefer id's engines, but I'm glad that Duke 3D was a success as the authors fully deserved their praises. All other things aside, the game was fast, skill oriented and fun, just like Doom.
It may have been squeaky, but it had far more features than Doom 2. Nothing is better than Doom 1 but I think Duke 3D is far superior to Doom 2. In many ways it's the true sequel to Doom, especially E2.
I too prefer Doom's more serious tone to Duke's mixture of violence and humor. Neither game's theme is better though - to each their own.
I find fighting mutants, pig cops and old fashioned styled aliens quite boring compared to Doom's demon killing.
For the same reasons I prefer Rage to Borderlands (gameplay differences aside). Rage is serious and that's how I like my games. I played Borderlands for a short time and all the time I felt like I was inside a Warner Bros cartoon.