Well the previous plumbers might have been cowboys.....or they may have been great plumbers but with the design sense of a manhole cover..... in my experience a lot of plumbers know that A has to connect to B.................but they are not so hot about the routing between A and B Laziness and lack of standards are rife!. Sure you could lose these pipes under the floor............get the floor boards up and have a look........plan your routes.......and get fitting, notching out joists as you go for the pipes.Don't put the nails / screws back into the same holes without thinking where the new pipework is...infact you can always mark the piperuns with a permanent marker on the floor above them to remind you and others where the pipes are ( unless you are going to have a stripped pine floor.........it might no look so hot:) :):)
another idea might be to create a "skirting box " to hide your pipes in if there is anyreason whey the cant go below the floor boards
good luck
Barry