I have used flux-simulator alone, so I'll comment on that. Overall, it seems to work good. But there are some issues with it. For example, PCR fragmentation set to TRUE always ends up with error. 1 out of 10 times, it still ends up abruptly because it accesses negative locations. However, overall I find it nice once you figured out these kinks. The documentation is very nice. Also, once you have a replicate (by providing the -x -l -s and -p parameters) you could prepare technical replicates by keeping the library and gene expression pattern constant and providing only -s and -p parameters and also biological replicates by keeping the gene expression (-x) constant (by constant, I mean copying the gene expression profile from the first run to the second one and not supplying the -x argument).