Checking bags is not a waste of time if you manage your time better. Instead of being out of the airport 20 minutes quicker, do something during the wait that'll otherwise take you 20 minutes later in the day. Cost wise you have to work out how many times you estimate you will get caught and pay a premium for gate checking against the cost to check it in upfront and see which you think is better.

Very occasionally a bag will get delayed. If you're heading home that's not an issue but if you're travelling look on it as an opportunity to spend the airline's money on new stuff for yourself. Always have a change of underwear and a t-shirt in your carry on to tide you over.

The self connect risk can't be helped unless you chose routes where it's not required, but if you're that close timewise then a small delay in your incoming is going to make you miss the next one anyway. That's probably a greater danger in your plan, particularly with LCCs.