I was playing around with some alternative boarding rules. Here is my concept:

when boarding succeed each ship received as much E counters as the other ships two leftmost crew slot numbers declare.
Plus if a ships burden is smaller than the other ones it draws as much additional E counters as the difference is.

Example 1:
Unite (burden 3) -> 2+1 (2 leftmost crew on HMS Meleager) = 3 E counters
HMS Meleager (burden 2) -> 2+2 (leftmost crew on Unite) + 1 (1 lower burden) = 5 E counters

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Example 2:
Unite (burden 3) -> 3+2 (2 leftmost crew on HMS Vanguard) + 2 (2 lower burden) = 7 E counters
HMS Vanguard (burden 5) -> 2+2 (leftmost crew on Unite) = 4 E counters

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With that alternative rule the number of left crew men has an effective influence to the boarding. Not only the burden of a ship.
For wave 2 ships it's now possible that even a small but fully manned Sloop (burden 1) can successful board bigger ships if there are only three or two crew slots left.