Also, why would mess with the Japanese invasion of Malaya?
The Japanese mad landfall in Thailand and at an unfortified part of the peninsula in Khota Baru. The amphibious part of the invasion of Singapore was across the channel on the Northwest part of the island where it's less than a mile across. The easy to fix this is to make the map so Singapore isn't technically an island, instead make the northern border a "Big river" for combat purposes.
So the map would be like this...
Sorry - should have used the term 'Malaya' instead of Singapore - you're spot on about the actual capture of Singapore (and I agree about the 'big river' thing re the gap between Singapore and the Malay Peninsular) - but in the case of ports exerting a radius of control based on the various assets available there, MTBs could operate upwards of 250km from their base of operations and longer-range designs used by the US and Germans over 500km. The British were aware of the Japanese convoy heading south, and had there been a significant MTB presence in the area then they could have potentially caused a significant amount of disruption to the invading force, either operating straight out of Singapore or using ports further up the peninsular to extend their range to intercept the invading force. The Japanese invading force was a light cruiser, a handful of destroyers and three troopships - you'd only need a handful of longer-range MTBs to cause significant disruption, and a sizeable force of smaller vessels available for interception could have turned back the invaders entirely. It wouldn't have been possible with British boats built for shorter-range work in the English Channel, but would have been by longer-range designs (and even the shorter-range British boats extend Singapore's area of 'influence' out from port by a factor of around 10 relative to just it's guns).
As it was, all Singapore had was it's fixed armaments, which were great if the invading force came straight at them, but hit anywhere more than a few kilometres away and they were useless.
So, in-game, if you had Singapore garrisoned with 'coastal defence assets' (a proxy measure that piles minelayers, minefields, MTBs, MGBs, coastal artillery and what-have-you) to a level similar to that in IRL of Cherbourg in 1944, say, it would have a much longer potential range in terms of intercepting incoming fleets (and not even need to piggy back off other ports up the Peninsular to intercept fleets arriving at Khota Baru). On the other hand, if you give Germany's and Britain's ports the equivalent of Singapore's 'coastal defence assets', and their capacity to intercept anything is very, very limited (Not that the D-day landings were a great thread, but it would be impossible with this kind of mechanic for the German player to even decide to go over-the-top with E-Boats as a coastal defence strategy).
So you've got two very different models of 'coastal defence assets', and if the game adopts a 'one size fits all' approach (where higher level = better and possibly greater range) it will make it harder to balance different theatres vis-a-vis historic OOBs and capabilities.
I'm not saying it's not a reasonable enough approximation to do the one-size-fits-all thing, as giving player's the kind of choices the different nations had in the war in terms of developing appropriate (or, in the case of Singapore, inappropriate!) coastal defences does add micro-management, particularly to people playing the US, UK and Japan, and to a lesser extent Italy, Germany and France. That said, I'd be in favour of splitting coastal defence into 'coastal defence buildings' and 'coastal vessels', to differentiate between the two different types of defence (as well as to make it possible to whittle down the coastal vessels defending the broader area, but not need to attack a port supported by coastal guns head-on, for example, or shift the MTBs to a nearby lower-level port that was under threat).
Done like air warfare, it needn't be anything too complicated or fiddly, and be largely hands-off, but it'd still be another thing to track, so I'm not getting all 'OMG, the game wouldn't work without independently modelled MTBs/E-Boats/etc;', but I think there's the potential to add meaningfully to the naval component of the game by having them in there.