I play all of the pet jobs fairly often and off the top of my head here's what I'd like to see:
BST
After the past few updates I can't really think of any huge change that is needed. I'd like to continue seeing new Jugs from 90-99. I'd also like to see the return to Charming mobs instead of just throwing jugs at stuff. Give me a reason to have all the charming gear I have =P. As others have already stated, I'd like to see more gear with buffs to the pet and masters both as well, similar to the Cirque Attire set.
PUP
This job needs much more than BST at this point imo. I'd love to see a new series of weaponskills for our automatons as well as some new attachments. I leveled PUP to 75 within weeks of the jobs creation (to the ridicule of many I might add) and I always looked forward to the updates because at the time they were adding loads of new attachments. IIRC they haven't added any since Coiler and Steam Jacket ; ; Another thing that SE has been much better about lately is giving us gear that is less "magey" and more DD. I'd like to see them continue with that... although I'll prolly piss a lot of people off, I think PUP should be added to MNK/SAM/NIN line of gear completely.
DRG
This job is already a DD powerhouse but I'd personally like to see more emphasis on the Wyvern. While I liked the additions to the AF3, I think even more focus needs to go to the wyvern for those of us who like to play the job "off the beaten path". Giving us more control over the wyvern would be nice. Maybe some more breath attacks/buffs that we can control like enfeebling offensive breaths (Frost Breath = Paralyze, Earth Breath = Slow, Lighting Breath = Stun ect...) and enhancing defensive breaths (Regen Breath, Refresh Breath, Haste Breath lol idk) even if we could only trigger those breaths when the wyvern has TP (similar to Ready for BST). I also would LOVE to see an ability similar to Dues Ex Automata for DRG. For the minor role that the wyvern presently play (offensively anyways) I've never understood the need for a 20 minute recast on Call Wyvern.
SMN
I'm having a hard time thinking of what this job needs atm. I think the job is pretty balanced in respect to the role it plays. I guess some things that would be a welcome addition from my point of view would be more Blood Pacts, both Rage and Ward from 90-99 (which we will no doubt get). I also would like to see at least 1 more Avatar added. Not so much out of necessity but just more options. I for one was disappointed with how Odin and to a lesser extent Alexander operated when released. Alexander is very useful at times but Odin seems very lackluster for the cost of our 2 hour. I'm not entirely sure which avatar could be added but something impressive. At 99 when there is a good chance BLM's will be casting Meteor and other jobs no doubt will have their flashy new abilities, I'd like whip out something impressive myself =) (an Avatar that is lol)