Its good to plan also what you want to see and intersect those on your route.
Ive been twice through Mexcico and once through central america, my favourite sites were the Pre-hispanic sites of Palenque, Yaxchilan in Chiapis, Monte Alban in Oaxaca, Tulum and Calakmal in the Yucutan Penninsula.
In Oaxaca there are some great rides through the state, especially up around where the old jesuit churches were (check the lonely planet where they are).
If you dont mind the heat, its pretty scenic through the Chihuahua desert from Juarez down to Torreon.
In the Gulf, the Olmec park and zoo in Villahermosa. Veracruz is a cool town too. Theres a cool ride through the mountains is from cuidad del maiz to cuidad valles, you basically change from high desert straight into tropical forests.
Yucutan Peninnsula, a jungle ride from Conhuas down to Calakmul was awesome.
Belize: I liked down towards the Maya Mountains towards Placencia
Honduras: Tegucigalpa to Las Manos is a nice mountain ride
Costa Rica: San Jose to Sixaola was a nice ride in the cloud forests and coastal tropics
Panama: road from El Lianoto Yaviza in the Darien was lots of fun
have fun planning