A minimote is a Z wave device, it has no way of communicating with either a Hue bridge or a Hue Bulb, as those are zigbee.
Hue bulbs are certified ZLL devices, nothing has changed between the first, second, or third generations as far as what zigbee coordinators they can connect to.
All of that said, there are several reasons to use the hue bridge if you want to use hue bulbs with SmartThings. See the FAQ ( this is a clickable link)
As far as the bulbs that you can’t connect, see if they will work with the hue bridge that you have. If they will, then you should be able to reset them and then use them directly with your SmartThings hub if you really want to do so.
If you can’t get them to connect with your hue bridge, then contact Phillips hue support.
What you do have them working with your hue bridge, you will still have to reset them. If you have a Hue dimmer switch, you could do it with that. If not, you can use the laptop method described in the following thread: