The main issue likely to occur in future is when the multi processor kernel for ZerOS gets enabled. The Orb mainboard has a dual core processor - the FLX has a quad core processor (if memory serves from a conversation with Jon Hole back before the FLX was officially released).
At release, only a single core was enabled (impressive that ZerOS does all it does on a single core!) - this was probably to allow the Solution desks to still run. Jon thought that the second core might get enabled when more extensive features got included in ZerOS - we had been talking about the "stage mode" from the Sirius 250/500 where positions of moving lights could be remapped dynamically by the software according to a "map" of the performance area held by the desk. I think also that some sort of media server might be envisaged to allow "simple" projection via multi cell LED fixtures (a bit similar to how Pixelines were used by Oasis when they played Glastonbury in 2004).
Aside from this - the only issue you're likely to have with an Orb now is going to be hardware support down the line. My gut feeling is to say if you can find an Orb for a stunningly low price, then buy it but otherwise - hold out and buy an FLX... To misquote Brian Potter from Phoenix Nights "FLX it's the future... "