I've already used php, mysql and js to make a maps-based guide before.
For that last project I didn't really have to use fusion tables: I
just went ahead with only displaying the markers inside a box a little
larger than the recommended zoom level for that purpose. (no more than
40 markers inside a 600x420 zoom 14 map)

I am somewhat experienced, but now I really need my new app to scale,
so I'm learning how to use GAE.

I know people use fusion tables for really high-density data.
Mine is not that much, but still like 50 markers on a zoom 16... so I
was considering using it instead of storing my info directly to the
datastore (using geomodel).

Asking this here is much more appropriate than on the fusion tables
group, since everyone here with geo-related projects had to deal with
this.

Which one should I use? What are the real pros and cons?
I'd like to know opinions from people who use any of those solutions
with app engine, but most specially if the person has already tried
both.

Thank you very much!

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