Anything lag related or crash related is from Bukkit. I am not sure about the other stuff. But you wouldn't be doing a better job. Well, its a possilbilty, but very slim.
Don't blame Jeb for all of this. Most of it is due to Craftbukkit. Jeb made a huge leap by joining together singpleplayer and multiplayer, and another huge leap in multithreading capabilities. One problem is that Minecraft coding is not written efficiently. Another problem is that in 1.3.1 a majority of the was rewritten due to the combining of multiplayer and singleplayer. After the rewrite of code, bukkit had quite a bit of changes to make. Just wait it out, and the bugs will be gone after some time.
I guess we can almost compare the current updates of minecraft to microsoft: Windows XP / Minecraft 1.2.5 - Stable and somewhat user friendly, but mostly reliable. Windows Vista / Minecraft 1.3.1 - Unpolished, glitchy, seems to have a multitude of issues, not user friendly. Windows 7 / Minecraft 1.3.2 or 1.4 - Hopefully mistakes have been learnt from and this is a great update.
I believe we are currently on bukkit--, waiting for a stable bukkit++ release to solve (hopefully) all the issues.
*waste* This is Minecraft, by playing it, your not doing anything productive, so its not like your not already wasting time.
I already know that mc is a waste of my time, I am saying I don't want the thing that is wasting my time to not be fun.
Yep got that part, but it is still pretty dumb how mojang did not decide go ahead and release a update that would fix these bugs.