In 2.10, it takes approximately 3 seconds to walk from the extreme left of the screen to the extreme right of the screen. In 2.10, it takes approximately 4.5 seconds to swim from left to right. In 2.5, it takes approximately 6 seconds to swim from left to right. Therefore, Link swims far too slowly in 2.5.
I'm not sure if this is related or not, but Link's swimming is a little glitchy, too. Let's say you line up Link to half a solid tile above him, such that the right half is solid and the left half is water. If you hold in the up and left arrow keys, Link freaks out:

The graphical bug: confirmed.
I'm not sure about the swim speed, though.
Nope, I'm using my 2.10 quest.
I guarantee that Link is swimming too slowly. The very first second Link swam I could tell something was wrong.
I am not sure about this one. When I was playing my quest earlier I didn't feel a lag in the swimming. It felt normal to me.
Here is a video explaining my case. (Please read the text below first.)
The left player is version 2.10 and the right is 2.5. In 2.10, I started swimming when Winamp (in the background) hits 5 seconds, and I reach the end with 9.5 seconds. Therefore, it took about 4.5 seconds to swim. For 2.5, however, I started swimming when there were 15 seconds, yet I reached the end with 21 seconds. That took 6 seconds, an entire 1.5 seconds slower than 2.10.
Does this bug occur in build 704?
704? Yes, both bugs exist, actually.
I wonder if this was the result of some tweaking related to drowning in walkable water.
Possibly; the swimming code in general appears to have been hacked on at some point and has become a nasty mess. I'll take a look.
I can confirm that both bugs are existent in 780.
Actually, the slow swim bug isn't a bug, but an intentional change in build 438, to make swimming behavior match the swimming behavior in Z3. Maybe a quest rule is needed.
Interesting. Yeah, I agree with the need for the quest rule, because a quest could become unplayable if it requires a timed swimming sequence to continue (e.g., Hero of Dreams, I believe), and Link swims too slowly to pass.
Wasn't this fixed in a recent beta?