@BadOmen, I didn't have access to the HP2 or Uniphy controllers (licenses), when I made the design, so I'm using the HP currently. By "match the burst counts of the DMAs to the memory" you mean the DDR2 memory I assume. I'm working with on-chip memory at the moment as this is faster and less complicated.
@Daixiwen. Actually I'm only able to burst transfer 8 kilobytes (2^13), since I have a Stratix IV GX ES. The reason for this is that the M144K blocks are bugged, meaning you can't use them in dual-port dual-clock mode:
http://www.altera.com/literature/es/es_stratixiv_gx.pdf. So (part of) the SMGDAs are implemented in M9K blocks, which aparently (according to the Quartus II errors), only support a width of 13. Which is a shame since the RapidIO core supports up to 32 kilobytes for the RX and TX buffers, so I could have done 32 kilobytes bursts if it wasn't bugged.
I think I will try to see if I can get the quick-and-dirty solution to work, since I have no experience with interrupts handlers in the NIOS II and I'm running towards the end of my internship period. I can leave the rest as recommendations in my report.
Thanks for all the help :).