I really cannot speak to glTF or obj, but coming to 2.80 and also from internal render to nodes is a really big step. Much bigger than which exporter you use. If you concentrate on using the
Principled BDSF shader, it will both make it easier, and allow you to go either way.
I think the .babylon format exports a larger set of data, like dynamic shadows or switching between std & pbr materials, than glTF. glTF can go to lots of places of course, but if all you are doing is BJS, you can just keep the .blend files around to keep you options open. You probably want to do that anyway.
One area of difference might be file size. Coming from a .babylon format you think might be in for sticker shock with glTF. Remember text files can use standard gzip transfer to the client without you doing anything so formats like .babylon or .glTF sizes should be multiplied by 0.3 when compared with .glb.
As you are new here (to the forum at least), this area might be a good spot for you to do some experiments, and let us all know what works and what does not, cause there is not much beyond “I like this way, but I have never tried anything else”.