If you want the stacking to still mean something, I can propose this:
1). All bases must either converted or proxied to a common base. we suggest the miniature base. (Requires mongoose to make cheap conversion bases for fleet action style figurines and establish fixed base sizes.)
2). When a player decides to move, he or she moves all the ships of the activation. In the case of a squadron, each ship is moved once at a time.
a). If the prospective final location of the moving object is in the same base area as one or more auxiliary craft, not in the same base area as another ship, and the unit moving is not an auxiliary craft, all auxiliary craft are placed on top of the base and of the newly-moved ship.
[Fighters and ships stack ... no anti-fighter bases for you! This reflects a slight upgrade for fighters.]
b). If the prospective final location of the moving object is occupied by an auxiliary craft and the moving unit is an auxiliary craft, the move is illegal and a new move must be found, including, if necessary selecting no movement at all.
[Fighters can only stack when escorting other fighters]
c). If neither of the above is true, and there is a final legal base location available within a small (here, fit your own house value, I'll say 1/8") distance from the final location that is on the current heading forwards or backwards, simply use that. If that is occurpied, itself, however, by another ship, use the procedure below.
[This is the fudge rule -- I'm only off by just a tiny bit, is that a problem? Nah, just place it there ... probably enough to resolve most situations right there.]
d). If the prospective final location base area is occupied by opponent ships only, the owner of the moving ship may select from the following two options:
1). The owner is allowed to continue, indefinitely, to the next point of relief past the ship blocking at the moving ship's heading until a suitable base space is found or another ship or ships is responsible for blocking the base, at which time this procedure is re-executed for the new situation. Movement in excess of that permitted is specifically allowed in this instance
2). The owner is allowed to cut short his move, at any time, to the next point of relief short of the ship blocking until a suitable base space is found or another ship or ships is responseible for blocking the base, at which time this procedure is re-executed for the new propsective move. This path must include any and all turns executed by the move in question. This is allowed even if the ship no longer has access to the All Stop special action, and may be in njunction with other actions, such as All Hands on Deck. It is not a special action.
e). If the prospective final location base area is occupied by friendly ships only, the opponent of the moving ship may select from the following two options in part d.
f). If the prospective final location base area is occupied by a mix of ships only, the party chosing the procedure in 2d is determined by who has more ships under the base. In the event of a tie, the opponent makes the selection (section d, above).
f). It is very possible, in congested situations, that this procedure may need to be executed multiple times -- one ship blocks a location that another ship needs, and so forth and so on. In this event, it is recommended that players not permit infinite decision loops of iterations of the process of 2d.
[Spirit of the rule: it's the blocker's fault. If you can only land on your own ships ang go where you want to go, tough, your opponent will choose where you end up ... enjoy. If you get blocked by an enemy's ship, you'll get the choice. Given that the moving ship gets to choose what the final unit that's blocking its path is, the latter is more likely. I give up that you can get something for nothing here --- All Stop plus another special action if you can arrange it, but it's a bit contrived, and you can't always select how much all stop you get. On the other hand, if you manage to create a situation where you're tripping over your own feet -- speed crits can certainly do this -- expect to get hosed. The Drakh swarms of raiders and boresight fleets can be particularly bad, here.]
3). If a ship is capable of movement, but for any reason is not purely able to a lack of base space available, this ship is considered to have moved an infinitesimal amount and is not a valid target for weapons with the Mass Driver property.
[No Dilgar cheese.]
4). As the situation becomes crowded, we recommend the temporary use of proxies or counters (which would have to be cut to circular base sizes now[!!!]) as temporary placeholders to protect the miniatures involved in the scrum.
[Common sense.]
Sorry for all the legalese, but this is my first attempt at cheeseproofing a rule that still keeps the base exclusion zones intact. Otherwise, the proposal is Animus' free infinite stacking idea.
