When farming waypoints, the higher levels give fairly good drop rates, but the champion minions can be very powerful. The maps in this post should help you avoid them as much as possible. There are three really good reasons you might be doing higher waypoints: farming for trinket materials, trying for the tier 3 (t3) trinket at waypoint 45 (wp45), or trying for the 50 gems at wp50. There are also players doing high waypoints (especially wp50+) just for the challenge. Which is good, because none of the awards past wp50 justify the huge effort involved in completing wp51+.
If you're farming for materials to make t3 trinkets, my advice is stick to waypoint 40 (wp40) and lower. There is not any significant advantage to farming wp41 and above, and you risk having to use potions for healing, which is really unnecessary when farming.
If you're going for the t3 trinket at wp45, you may have to use some potions, but use these maps to minimize that. Pick your strongest element-matched allies and equip your best gear (I find that high dodge works best, depends on your fighting technique though). Do not ever use revives: if you have to use a revive to make it through a waypoint, then you're probably doing a waypoint beyond your current level/gear/ability. Work on something else in the game, then try again once you've powered up.
If you're going for the 50 gems at wp50, think of it as a way to convert potions into gems. Use as many potions as you have to. I can do the run wp46-50 with about 5-10 potions now, but when I first tried it took me 120 potions, and I have heard of players spending over 200 potions. As I said above, do not use revives. You're getting gems, but don't waste any on revives. If you run into trouble, then give up and start the waypoint again, preferably on the first or second room (1/5 or 2/5). The routes below should help you avoid champion minions. Spirius and Harbinger are especially bad, but any champion is extremely tough past wp45.
The most important thing playing waypoints is to know the map. The map below shows all the rooms, with each of the the six possible starting points indicated by the blue circled numbers. The most champion-free starting points are 3 (23% chance of starting there) and 2 (16% chance). Starting point 4 (12% chance) is also fairly good. Starting points 1 (16% chance) and 5 (14% chance) are considerably worse, and starting point 6 (19% chance) is by far the worst of all. When facing a really tough waypoint, I strongly recommend giving up and trying again if you're given a start at 1, 5, or 6 (I also do that for 4).
Beyond the starting point, it's important to consider which rooms are the most dangerous. The next map shows the probability of meeting a champion in a given room, which varies from the safest rooms at 0% (no chance) up to the worst room at 71% (very high chance). The green rooms are always champion-free, the yellow rooms are almost safe, the orange rooms have about a 1/3 chance of meeting a champion, the red rooms have about a 1/2 chance, and the red rooms with the red outlines have a significantly greater than 50-50 chance of meeting a champion. When running waypoints, you'll obviously want to avoid the dangerous rooms and stick to the safe rooms.
There are over 58 possible routes through the waypoints, but I have only tested the 58 most obvious of them. Other possible routes involve sneaking through rooms without starting a battle, and will be added later. In order to talk about routes, the rooms have to be numbered.
The best overall routes are 301-302-701-412-702 (47% chance of getting through without meeting a champion), and 201-202-701-412-702 (40% chance of getting through without meeting a champion). The worst route stands along with just a 2.6% chance of not meeting a champion: 601-512-602-601-512.
Instead of odds, the average number of champions met can be considered instead. The same three routes are best and worst: 301-302-701-412-702 (0.61 champions on average), 201-202-701-412-702 (0.79 champions on average), 601-512-602-601-512 (2.40 champions on average). The sorting isn't always identical between the two statistics, but it's very close.
Beyond the best overall routes, are those with a high probability of a champion only in the first or second room. For the toughest waypoints, it's handy to be able to give up and restart when you meet a champion, but only if you haven't wasted too many potions already. If you neglect the first room, the best route is 201-202-701-412-702, with a 60% chance of not meeting a champion in the last four rooms. If you neglect the first two rooms, three routes give a 79% chance of not meeting a champion in the last three rooms: 201-202-701-412-702, 301-302-701-412-702, and 311-312-702-412-701. Since the first two of these also give the lowest overall chance of meeting a champion, choose 301-302-701-412-702 or 201-202-701-412-702.
The following table lists all 58 routes (that have been tested so far), sorted from best to worst in terms of the odds of getting through the entire route without meeting a champion. The other quantities outlined above are also shown.
The above maps and probabilities are based on 58 runs through every possible waypoint route (except that I missed a few past that 58; they'll be added shortly), plus an additional 53 runs to get better statistics on the starting points and some of the rooms. In the current set of data, each room has been sampled at least 11 times. All of the test runs were done on wp36 through wp47; there doesn't seem to be any pattern to start points or champions, all waypoints seem to follow the same random probabilities (that doesn't mean there isn't a pattern, just that I couldn't see any).
If you have any routes to add or spotted any incorrect advice or errors here, please let me know.