For the TKO-Ma On Shan route, I think there should be two routes: Po Lam/Hang Hau and TKO to Ma On Shan so passengers from North TKO won't have to change buses, which is another pro in this situation as you've also got to compete with the MTR. Or else, passengers from North TKO would likely want to take the MTR instead as it is more direct. There should be limited stops (only main stops) in Ma On Shan to raise efficiency.
For the TKO-Yuen Long route, you should stop at Tai Po, Fanling and Sheung Shui (like W3 stops) and at last Yuen Long. Would you consider extending it to Tin Shui Wai and/or extending 290 to Tuen Mun?
Personally I don't agree with the route going via Lam Tsuen Road because it takes so long and it would require a smaller bus which is not efficient. Also, the road has a lot of curves which increase traffic accidents and people might get dizzy.