Sawsall. GH construction crews us ethem all the time.

I see that this is an old thread that has been revived. The OP hasn't posted here in more than a year. But anyway; I have used a circular saw ("skill saw"), with the standard blade that is used for cutting lumber, to cut both multiwall polycarbonate and 1/4" thick polycarbonate.

Manufacturers recommend, and I have always used a saber saw. The problem I foresee with any high speed tool like a roto-zip is melting the plastic and clogging the bit.

These manufacturers and vendors suggest or recommend standard woodworking circular saws:
http://www.plexiglas.com/pdf/guidelines.pdf
http://www.sheffieldplastics.com/web...02_Mak_Fab.pdf
http://igcusa.com/catalogs/Multi%20Install.pdf