Take either. It doesn't matter.
The big difference is that on the £16 train fare, you can take any train that day and break journey if you want- at Falkirk for instance, or Linlithgow.
The £4.30 + booking fee you are tied to that particular bus. So your plans are inflexible.If you are OK with that, and are price sensitive go for the bus. Most of the seats are upstairs.
Don't expect your bus to be Megabus liveried- it might be but is far more likely to be in blue and yellow City link livery.
Even if you buy the more expensive tickets from City link it is a specific timed departure you book, and the same buses (literally) you travel on. This is a code share route.
Mix and match your transit options in Glasgow to suit your plans. I think that Glasgow is a city where HoHo actually works, and works well.
The Glasgow Subway is useful for some tourist journeys (the Clockwork Orange as it is locally known). They are in the process of introducing a new fleet of trains- some old and some new presently.
You could just ride it for one circle, for the experience, even if not using it as actual transit.
Also many of the sights are in walking distance of each other. Walking has its own rewards for appreciating the built architecture.