Ok, following that logic, these 3 Thunderbolt ports can be anything anyone wants, including 4 Thunderbolt ports. I mean if you are happy using dongles and docks, you can have as many Thunderbolt ports as you want (well up to 6 anyway, if you want to keep the same bandwidth as previous generations of MacBook Pro).
I honestly can't tell what is your loss here. If you don't like SD card slots, MagSafe, HDMI, than do use it. You have 3 full channel Thunderbolt ports than can be anything you want. You can even charge from them. There is no functionally removed for you.
Meanwhile, for the rest of us who like having things built in for diverse needs, we have more options.