Aside from the actual code, phpMyAdmin works quite well. What are you going to change feature / UI wise?
What I "would" change (never agreed to re-writing it myself

):
1. The interface is cludgy and old-school. Clearly built in the 1800's :p
2. It's slow, hard/impossible to modify and uses FRAMES which always caused me headaches
3. Last I heard/read (may be wrong) PMA wasn't being regularly maintained
4. Migrations support
5. Views/Stored Procs/Triggers/etc I don't think were supported when I last used PMA
There are literally a 100 things I would change about PMA to large of a list to compile on the fly while at work and doing something else
SqlYog is a vast improvement but has some draw backs. Enterprise is a step in the right direction but is not "sweet" enough for me to justify the price.
I frequently want to rename columns and re-order columns. UI than facilitated drag and drop would be stellar. Generating migrations would be a bonus as well. Schema print-outs, GUI designers, transactional support, etc.
I don't think PMA holds a candle to most desktop software other than it's web-based and MySQL being predominently used in a web environement I think many developers would prefer web based SQL manager.
Cheers,
Alex