Sorry this is a bit long of a post.

We have been to all three resorts, Conrad Maldives in 2017, Conrad Bora Bora in 2018, then Waldorf Astoria Maldives earlier this month. For reference we have also stayed at the Intercontinental Thalasso Bora Bora in 2016, 2017, and Sheraton Full Moon Maldives in 2012. We have also been to Seychelles in 2016 which we think is fabulous including the world's best beach Anse Lazio and some of the clearest waters I have seen if one wants to snorkel / dive (for us supervised snorkel tours).

It is too simplistic to say which is the better resort so I will try to keep to the main points I feel might change which one chooses over the other.

For points stays; the Conrad Bora Bora is the weakest out of the three where you could end up in the Garden View Suite you have booked. Sure they are nice, 100sqm in size, but they are more like studio apartments with common walls with other neighbours. The Conrad Maldives then have the options between Beach Villas or Water Villas which feel more like a resort island holiday, they are genuinely nice until you see the Waldorf Astoria Maldives, sure there is a slight points premium but these beach villa with pool blow everything out of the water.

For dining, we found Bora Bora dining to be weakest (in terms of choices and quality) out of the three including that at the Intercontinental Thalasso. The Waldorf Astoria has better quality of food out of the three but the Conrad Maldives have dining experiences that the Waldorf Astoria is lacking, such as beach BBQs, beachside japanese grill, being able to dine over the water at Mandhoo, Sunset Grill versus the only over water dining option at WA is Li Long which has four tables and very little overwater ambience. Conrad Maldives you can then dine under the water but the WA you can sit in a bird like cage. Also the WA you are paying 15-30% more than Conrad Maldives generally, and Bora Bora it would have been a further 5-10% less than the Conrad Maldives. WA lacked an island resort feel sunset bar (sure they have the Nava Beach Bar and Amber) but I didn't get sand between my toes and that made it less appealing personally. Both Conrad and WA have an underground wine cellar but to enjoy the latter, you had to spend $300++ pp (or three times than the Conrad eg. cheese fondue) to get the chance to do so.

For service, Maldives wins hands down whilst the locals at French Polynesia operate like its "island" time. Some FP resorts try to employ as many locals as possible but that could either give it a more "local" feeling but losing service (or brand) standard so they need to find the 'right' balance. Now the WA has superior service to the Conrad Maldives but maybe the resort is new, the staff are excited and welcoming, and guests are happy to be there. There were little things that WA staff did (actively opening doors, actively helping with bringing things to the table, meeting guests request even if its not listed) as an advantage. If you wanted something, consider it done.

For the main resort pool; the WA's family pool is gorgeous and wins easily out of all three properties. They also have a long 40 metre adults only pool which is great for laps. Both pools were often close to empty because all the villas have their own private pool. The Conrad Bora Bora pool is decently sized and felt inviting and hence I rank it second. The Conrad Maldive's pool is third because one, it is affected by sea planes and noise and two, it can get crowded because it is such a small pool. Similarly the adult only pool whilst nice, have limited seating.

Now for pricing, you said getting to Papeete or Male is similar so let's look at a rough estimate in cost from said airport to resort:-

Papeete to Bora Bora return flight $500 plus Conrad Bora Bora shuttle (or the free local option).
Male to Conrad Maldives $560++
Male to Waldorf Astoria $700++

The Waldorf is slightly more expensive here, however comparing the Maldive properties, the benefits is that taking the Waldorf Astoria's yacht means you can get to the resort by 11am resort time (they're an hour later, thus you get the first yacht that departs 9am Male time), you can leave the resort as late at the 11pm boat (that connect to SQ flights for example). The Conrad Maldives you are subject to lighting because sea planes only operate in day light, and last flights leave 6pm? or so.

The major benefits I see with Bora Bora is that you have access to main island and top up on snacks / food / alcohol. There are a variety of restaurant options (some touristy like Bloody Marys but hey why not). There is a variety of land tours / excursions / rent a buggy and cruise around the island etc. Also before/after Bora Bora there are other islands you can visit like Moorea and a few dozen more options. You can BYO duty free alcohol to French Polynesia (four bottles of our champagne of choice and two bottle of spirits between me and my wife - buy mixers when we are there). You can't BYO alcohol to the Maldives if you drink or its negligible if you don't drink.

Now the trick question is what would I like? Gosh, in my ideal scenario, I would love the WA's amazing beach villa with pool PLUS the Conrad Maldives dining options (happy to forgo some quality for island ambience) PLUS the resort transplanted onto the Bora Bora motu where the Intercontinental Thalasso currently is - the Thalasso has the most amazing postcard views of the lagoon and Mount Otenamu that Bora Bora is renowned for in my opinion. Oh and just to throw things into the spanner - beaches and crystal clear waters of the Seychelles.