Your Skeletal Options
You can create bloody skeleton and burning skeleton variants (but they cost double HD) you may also with the DMs approval create gnoll (or other creature) skeletons with the skeleton template (2 HD for a CR 1 in the gnoll skeleton case). It is noted in Battle of Bloodmarch Hill page 84. that with animate dead and an available dead vermin exoskeleton you can raise it with the exoskeleton template (I think this fits well with your only skeletons theme and technically vermin are not intelligent anyway, so you can argue that there is no torture of souls, however as the dark wanderer pointed out vermin RAW have a soul in PF).
Two more things in line with your bonomancer theme could be the Bonestorm (CL 19 Create Greater Undead) and the Wyrmskull template from The End of Eternity page 89. (It says “An undead creature created from the enslaved mind and spirit of a powerful dragon” but you may be able to have their consent to this as they can retain their alignment in their new undead form; the example has a chaotic good alignment)
Mohrg (CL 18 Create Undead) can be another skeletal option but I think it is starching your ‘skeleton raising is not evil house rule’ too far.
Non Skeletal Option
Another thing that you can petition for your character is to have an undead type similar to the deathless from 3.5 Eberron Champaign Setting page 275. in the world.
undead represent a mockery of life and a violation of the natural
order of life and death, the deathless merely stave off the
inevitability of death to accomplish a righteous purpose
They are the good aligned version of undead (animated with positive energy and not negative) and you might justify their creation by raising victims of a great evil for example and letting them fight against it to save their still alive family or their loved homeland.
About the mob template you have a few option. You can use the Creature Swarm or the Hivemind Swarm (may involve souls) template or if you want something more battle squad-like you can use the Troop rules to make something like that, but you should ask the DM for an approval.