Vaishali has a practical TT for a 110 km/h train (5:45 hour run), is non-stop and if delayed by a few minutes, won't have to worry about being overtaken and further get delayed.
Mahabodhi has a ridiculous TT for a 110 km/h train, both to Aligarh and then even worse from there thru Kanpur, amounting to an impractical 5 hour run. It is also closely followed by Bihar SK which has a reasonable schedule (like Vikramshila, 6 hours).
The SK can be expected to run on time. Mahabodhi cannot. And that means,...
more... it will be overtaken by SK, delaying Mahabodhi. Now, that it is already delayed and has overly aggressive TT thru CNB, it gets killed by other trains (even if not overtaken, 93 km/h average is very high for a normal schedule). Hence the delays. Mahabodhi would do better if it were slotted behind SK, and expected to run the distance in 6 hours.