Aren't there plenty of parking lots to build on before we even think about evicting Home Depot (a busy and well-used store)?
I would rather see the home depot build a new store on one of the lots, the building its in has some great old bones and would be better used as lofts or something similar, especially if it ment activting the streetwall along arsenal st. The drop celing in there hides some awesome supports, dormers, and skylights. The original crane is still hanging next door in golftown too. That is also the worst laid out home depot I've ever been in, and they have NO room in receiving.
While the HD would be a loss, you can get everything in there right around the area. There is a lumber yard on Arlington St, hw foot (paint) mahoneys (gardening) and granite city (electric) and an appliance place are all on western ave in brighton, target has most of the cheap shelving/storage/cleaning shit, and I'm pretty sure there is a plumbing place around there too
Regarding old bones, that parking garage has some really cool mushroom columns and flat floor plates, I could see it being converted to residential/commercial too, with a new, purpose built garage being put up somewhere else, preferably more centrally located.
As for the tunels, I don't know much. I assume they were for steam and utilities, im not sure how extensive the network is. There is a pretty obvious bulkhead for them facing the river along n beacon st, but it appears to be sealed up well. I poked around the utility corridors in the mall and had no sucess finding a way in
Edit: regarding the HD though, they aren't going to leave without a fight. Its neck and neck with south bay for the top store for the entire region. Their summer and back to school sales top a mil a day without breaking a sweat. There was also talk that a lot of the money that was spent to fight lowes moving onto the site where new balance is building came indirectly from HD, although I have no evidence for that. So, I'm pretty sure that even if they leave that building (which I hope they will), they are not leaving the immediate area.