If you don't mind fees, campground reservations and crowds I would combine the 3 best hikes the Banff area has to offer. I have done most of this individually but want to link up the hike eventually.
I would do the Mount Assinboine area, the Banff Highline (Citdel, Healy, Whisling and Ball pass / Egypt lakes area) and the Rockwall.
Stating at the Mount Shark Trailhead day 1 to Magog lake (29 km). Day 2 Side trips from Magog and hike to Og Lake. Og lake is only 7km but at a minimum you want to go up Nub peak 7km and then you could do another hike in the area or you could push ahead furthur to porcupine campground. This day could be as low as 15km and up to 30km. Day 3 to Citdel Pass 20 km. Day 4 to Ball pass 24km. Day 5 to Floe Lake 25km, Day 6 to Tumbling Falls 17km, Day 7 Out 28km.
If that is too many days another options would be to start at the twin lakes trail head and hike south over Gibbon Pass towards Ball pass on day 1 20km and then over ball pass to flow lake and the Rockwall on Day 2, Day 3 to Tublimg Creek 17km, then day 4 you could add a side trip to Goodsir pass and camp at Helmut falls 20km, and day 5 out 20km. From a car shuttle point of view this would leave you about 15km from your car and could be easily hitch hiked. This would remove the entire Mount Assinaboine area from the trip. Or you could leave off the Rockwall end of the trip and do the first 4 days as in the first route and on Day 5 hike out over Gibbon Pass and out the Twin Lakes trail head.
I would choose to do the Assiniboine area over the rockwall.
There are car shuttles from Banff to the Mount Shark Trail Head but that still leaves you from the end of the rockwall to banff. The various comapanies in banff will do custom shuttles for you if you are willing to pay or Hitchhiking usually works to get back to banff but would be more difficult getting to the mount shark trail head.
If you want to do 2 shorter trips I would do the Rockwall (Kootany National Park) or Mount assiboine starting at the Mount Shark Trail head but exit just after Citdel pass down the Sunshine Ski area access road which leaves you a quick shuttle back to banff.
The you could do one of a few trips in the Jasper area. The Skyline which is only 44km but makes a nice 2 day trip. Some trail runners will run this one in a day. Another really nice option is the Mount Robson area to berg lake and up to Robson Glacier. Day 1 you would hike to Berg Lake 22km, Day 2 you can day hike in the area 20-30km, Day 3 hike out.
Depending on logistics and car shuttles I think it makes more sense to do one longer trip then 2 shorter trips. The first trip I propose is all world class scenery and is the one I would probably do. It would be quite strenuous especially the last 3 days of doing the Rockwall.
edit: One more thing, My favourite guide book for deciding on what trips to take is "How not to Waste your time in the Canadian Rockies" It has good info on all of the above trips and many others plus the best day hikes as well and covers all of the Canadian Mountain parks.