Strictly speaking, there hasn't actually been a formal "answer" provided, so I will respond here (instead of the two comment threads):

I realize that this is what the developer has said to stop using TopHat, but I have definitely seen situations where it was helpful to use a TopHat alignment over a STAR / HISAT alignment. For example, I think some programs may have been developed with TopHat alignments (I know of at least one case I had to use TopHat2 to validate a known splice junction difference), and the more stringent alignment requirements may be useful if you want to avoid aligning contaminants.

In most cases, for something like gene expression, I think you will most likely get similar results (so, if you already have a STAR / HISAT alignment with reasonable results, you probably don't need to also test a TopHat alignment). However, you may also find that if you have something unexpected with a TopHat alignment, then I think there is a decent chance you may see that same trend with the STAR / HISAT alignment (although I would say that is a situation where it may be worth testing the effect of the aligner for your specific project, even if that ultimately doesn't change the result).

However, to answer your original question, I would usually run TopHat2 with 4 treads and 8 GB of RAM. I don't usually run cufflinks/cuffmerge, but it may be worth testing unique-read quantification if something about the transcript estimations doesn't seem right (but I think having replicates can help make the less accurate estimates less significant, at least if you are using unique counts).