The boot space doesn't matter to me. This will be used as city car to and from work. Rarely ferry passengers in back seat for long distance. To me the car is to get from point A to point B, at the same time I don't want to feel tired from driving.
The myvi feels slightly more comfortable to drive than the Saga, but the saga has modern features that myvi lack.
Which will you go for if you're in my shoes?
MyVI will give you pain free ownership (if you don;t get a lemon unit) but will cost a bit more than the Saga to buy & own (wear & tear items are more expensive).
Saga will give you low cost ownership, but dealing with the Service Centre is a pain that you will go through every 6 months.
For your 'I don't want to feel tired from driving' requirement, I always believe Proton have the best seats in its segment. Not too sure why you find MyVi more comfortable, but I always have backache with Peroduas after a long drive. Maybe the seating position? And the 2019 Saga should come with better insulation for better NVH compared to MyVi.
Any how, good luck with your purchase & ownership.