You want to land a substantial amount of, ahem, shit in there, since don't just want it to colonize one portion of the gut, and it's got quite a lot of competition.
So you would be talking a truly astonishing number of pills, I think, to compare to the volume you can manage with a tube.
WP suggests that it's about 100g (or 100000mg) of actual feces then mixed in a larger volume of saline or milk, and you'd probably need to have additional volume for assumed losses and whatever coating you think would work.
Good point, but shit seems to be made of a lot of stuff- ~75% water, undigested food and fiber, fats, inorganic matter... Bacteria seem to be about ~30% of the dry weight. So of those 100 grams, you'd get maybe 7/8 grams of bacteria? If so, these could possibly be delivered by a number of small capsules taken in the course of several days.
There really isn't. From the mouth is basically the same distance and it contains teeth and a tongue. Through the rectum is much much much farther through meters of intestine. Through the skin creates a surgical hole that's going to be difficult to keep sterile.