Still very much work-in-progress, but I'd like to hear any comments or ideas that you might have.
No need to install, just visit here to see TopHat's interface: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_se1
Main differences from the existing TopHat tool: 1. Far fewer visible options 2. Select "Existing gene mode" (use GTF file) or do De-novo junction detection (or both) 3. Allow insertions/deletions detection (with the latest tophat). 4. Allow user to specify custom command line parameters. 5. Accepts Fasta, FastqSanger, FastqIllumina (but not generic "fastq", per your feedback).
If you think there are other critical and often used options, let me know.
updated code is available here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_1.tar.bz2
-gordon