Basically, something will have to give. You can't make both the CS connection on the west and the Capitol Limited on the east, but which connection do you screw then?
I agree with building in some layover time midroute - add some buffer time at each of the smoke breaks. When the train is on time, it's sometimes nice to walk around for half an hour or so to stretch your legs and get some exercise, and maybe even a quick meal at one of the restaurants in a small town. Of course, for people that make the trip regularly, that could be annoying to just sit in, say, Minot for an hour.
Take out the CS connection, keep the CL. Because the CL is a direct link eastwards, while the CS runs at a right angle. Passengers that really need to get south from PDX can ride a Greyhound bus from the station (GLI-PUT) right besides Amtrak-PDX.
Passengers between PDX and VAN can ride the Cascades.
The other argument, though, is that the LSL could serve as at least somewhat of a replacement of the CL connection. There's no train service from
PDX EUG south other than the CS. Some people have an aversion to buses, and Amtrak may find it wiser to preserve as many train connections as possible, and the LSL is a more adequate replacement for eastbound connections than the Cascades is for west coast connections.
Edit: I forgot that some of the Cascades run to EUG.