I'd call it adding boat dives, not upgrading. Do it or not it's a lot about how you like to dive and spend your time and to a lesser extent your experience levels. Bonaire is all about the freedom to jump in anywhere anytime.
We went last spring and never got on a boat. Our Buddy Dive package actually included 5 1 tank trips and we couldn't be bothered. There was more than enough to do and we did it all at our own pace. That was us, shore diving from the back of the truck is what we do and consider that easier and more care free than boat diving.
If you are the sort of diver than likes to follow a DM or your trip will not be complete without seeing a frog fish and seahorse then by all means arrange to be on some guided dives. Being on a boat dive provides this. I'm more about serendipity. Next trip we do intend to work Klein and a pier or 2 into the schedule if pier activity permits.
We ended up doing lunch daily at the Buddy Dive pub by the sea or whatever they call that hut. Our package had a 50% discount on the first $200. and we had nice lunches for small money. It forced a good midday break and still left plenty of time for 2+2 dives with the evening to unwind/dine out or make a night dive.
Our plan was to get sandwich fixings but we arrived on a 3 day holiday with the market shut down. By the time it opened the pattern had been set. Next time I'd still try to go the sandwich fixings route of logistics work out.
Have fun,
Pete
