Both immediately doable suggestions and radical ones
First of all, the significant stations in terms of design have to be restored. The 1978 stations of the Spadina line need some restoration work:
Yorkdale should see its stainless steel cladding replaced and a thorough cleaning of the concrete. The brilliant artwork by Michael Hayden should be rebuilt, with LEDs being a good idea to replace the more problematic neon lights.
Wilson could use full demolition; it's not architecturally significant and has numerous usability issues.
Glencairn should see its artwork redone as well: that cathedral-like motif of coloured glass by Rita Letendre called "Joy" restored to its giant skylight.
Dupont needs the grout of its tiles somehow cleaned for a more consistent look. Eglinton West's small plaza in front of the entrance needs to be repaved with something similar to the original.
Spadina's backlit platform signage has to be turned back on.
All Bloor-Danforth stations could use enhancements like artwork, more benches of an attractive and comfortable custom design, more variations in interior materials, some flowers in summer and landscaping, and high capacity bicycle storage systems because the lack of secure parking at stations discourages many from cycling to the station. Dundas West really needs a second entrance on the east side of Dundas, because the number of people who jaywalk even without any gap in traffic is quite high. It could also use a connection to the GO line.
More radically speaking, downtown Yonge stations would also be more pleasant with higher platform ceilings and wider platforms in general. This is more radical in that it would require lots of renovations, but they might be necessary one day because of nascent water or structural issues. Also, stations with side platforms would look better without centre pillars at platform level. I'd love to see St. Patrick get green titanium panels as kind of nod to Gehry's signature material.
All downtown stations should also get covered entrances and use the opportunity to implement some distinctive design on that end.