Why does the F-111 have a capsule ejection system rather than a conventional system?
The reason the F-111 has an ejection capsule is pretty weird in itself- its there because USN wanted it.

In 1960, USAF asked for an aircraft capable of supersonic flight for 400 miles, and capable of operating from short/unprepared fields and capable of crossing Atlantic unrefuelled through Specific Operational Requirement (SOR) 183. At the same time, USN was trying to develop a fleet defender for its carrier groups which had high loiter time (> 6hrs) and can detect/launch missiles at incoming bombers and sea skimming missiles at over 100 miles. To this extent, the Douglas F6D Missileer was proposed, which got cancelled in 1961.

Unfortunately for USAF (and lot of others), US SecDef Robert McNamara decided that both these requirements could be met by the same aircraft- actually, the only things they agreed about were that the aircraft would have swing-wing, have two seats and have two engines. 

The USAF wanted tandem seating, while the USN wanted a side-by-side seating for improving crew co-ordination sharing the large radar display to launch missiles (like the A-6 Intruder, which had side by side seating, but conventional ejection seats). The reason the ejection capsule was included was that USN believed that it would give better chances of survival in case of ejection over sea (where it was to function as a life raft) and in high speed ejection. The USAF hated this as it increased the weight by over 500 lb, affecting performance.

In fact, the Boeing proposal included conventional ejections seats, which was required to be changed into a capsule (and was selected before McNamara intervened and selected the other one). In the end, USN escaped from the project (ironically due to weight and performance issues), while the USAF and others got stuck with the ejection capsule, which they never wanted in the first place.