OK, found some time and came up with this:
download spirit3t3a (rc1, 11MB)
Everything ix-ir suggested and some other minor things were changed:
changes spirit3t3

spirit3t3a:
* replaced the 2 teleporters between PG and LG with a short corridor
* removed mini-corridor leading to upper teleporter
* removed useless stairs at upper teleporter
* switched PG and LG positions to seperate RG from LG
* made RG platform bigger (thus making the jump to RG shorter)
* replaced glass above RA with grid to allow for interaction between the 2 levels
* removed decorative pipes in the floor at top level
* removed glass at all weapon markers
* removed lights at lower level of MH room that allowed ramp jump to upper levels
* removed concrete ramps in new PG (former LG) room that allowed ramp jump to JA and RG
* adapted jumppad targets so you'll land on the target spot without having to use air control (all JPs)
* sank JPs into the ground (no height difference from floor anymore)
* added 2nd entry to RA room from SG area
* added curves in a couple of places
* added botclips to allow bots to go for RG/LG ammo in MH room
* removed blood decals except for teleporter exits
* adapted lighting in MH room
* more clipping on the lower level
* made +25H near RA TDM-only
* fixed a spawn point (needed rotation)
I think the map feels better than before, especially the second entrance to the RA room and the grates instead of glass were a good idea.
Let me know what you think about it!