I commute nearly daily from Chester to Manchester and I'd say that (tatty seat fabric aside) the journey in is better than some first class journey's I've had. Getting on at Chester means that there's no issue with getting a seat at a table and the commute is quite pleasant until Newton-le-Willows where it's full and standing and more for those poor souls.
Now, I do take the 6.40am train which means that I get in just before 8 but even the later trains have seats at Chester.
The way back is more stressful - the scrum at Platform 14 in particular but I've never had an issue with getting a seat on the Chester/North Wales trains.
As has been mentioned previously, it's possible to make a connection at Crewe which is Virgin-[Change at Crewe]-Virgin and has first class. A longer (by 10 mins or so) journey but you can use the break in Crewe to pop in to the First Class lounge, grab a coffee and pastry, and be on the next train to Manchester.
Chester is a lovely city (although I don't live there) and if a longer but more luxurious commute is what she's after would suit well. As others have said, she may regret not moving to Manchester centre on the cold mornings despite all the free coffee.