I don't see necessarily a problem with 5000 coins.  It depends on how they are linked together (through distributed exchanges).  The lightning network can abstractly be seen as "as many coins as there are payment channels" in a certain way, where the "coins" are virtual block chains you build with the successive instructions on the payment channel.  Coins that "start out" when the channel is set up, and "die" when the channel is settled.  They get their value by using a collateral (the bitcoins engaged).  They die when they release the collateral. 
In the LN, all the "new coins" are of the same type, defined in the same way with a uniform (centralized ?) protocol.  But you can see "small coins" as totally anarchistic versions of this, where every other coin has other principles, engages another collateral (another coin, maybe bitcoin, maybe something else) on some distributed exchanges, and can release to *other* coins on these exchanges.

To pay for something "far away in coin space", you'd have to hop over several exchanges, like in the LN, you hop over several payment channels to reach destination.  But at least, contrary to the LN, things wouldn't be frozen in, uniform, ... Yes, there would be a need for some "standards" linking them.  But like in the technology world, the standards serve to interface different systems, but at least, systems of different types, with different technology and features, and innovation is possible.  The internet has standards, but the things connected to internet are of different nature, and evolve.  Bitcoin's tech is getting old now.  It can still serve as a kind of backbone, reserve currency in a way.  But it will never be able to handle all commerce all over the world.  Its monetary model is also problematic and it will end up being totally centralized because of economies of scale. 

If we want a distributed system, we need constantly new tech, new coins, and competing systems.  Not a monopoly.