Playing through the campaign, I found that especially any time I was tight on time or delta-v or having to deal with out of plane maneuvers or needing to arrange a difficult intercept, plotting out the exact maneuvers I needed with the necessary accuracy ranged from annoying to next to impossible, even if I knew exactly what I needed to do and how to do it. Additionally, the built in intercept assist can be very, very inefficient due to starting too late. Aside from the whole "n-body problem is kind of difficult and approximations aren't perfect" thing, these are solvable problems. In fact, some of them are at least partially solved in game, because the AI is able to do a better job of aiming missiles and doing intercepts than the player can do automatically.
What I'd really like to see is three-fold: a field you can open for text entry to directly define a burn, improvements to the automatic intercept and rendezvous tool, and a set of utilities for arranging hohman transfers, calculating longer distance intercepts, aiming missiles and so on akin to the tools mechajeb adds to Kerbal Space Program.