First, I think of all the twin name themes you could have, alliterative is one of the least annoying (this coming from someone who loves so many A names I could easily end up with alliterative twins by accident, just by using my next two favourite names.
That being said, I don't like the idea of passing up a name you love just to fit a theme, or limiting yourself if you don't love any thing else with that letter.
Secondly, I'm really bass at J names so I don't have many ideas, but maybe:
Jake &
Josh (
Jacob &
Joshua?)
Jake &
JoelJacob &
JonahJake & Judson
Jake &
JamieJacob &
JasperJake &
JetJacob &
JeremyJacob &
JeffreyJake &
JarvisJacob &
Jameson /
Jamison
That's a tough one.
Jacob is definitely easier to pair up.
http://www.behindthename.com/pnl/56287