I've dealt with this question among my customers for YEARS! It is a common mis-conception that most 3" guns can equal 3.5" if both are set up properly. I simply haven't found this to be so. BUT the keyword there is "setup properly". ALOT of people who tell you that their guns pattern 3" loads better than 3.5" loads are telling on themselves. How? Because such conditions (same with 2 3/4" vs 3" guns) point to choke restriction. Putting a bigger/faster load through a super tight (under .660 in most guns) will produce blown or "donut ring" patterns with big 3.5" loads. ESPECIALLY when talking about lead alternatives like Hevi-Shot, Nitro, Win. Extended etc...
You can take some .640"-.660" tubes and produce some impressive patterns with 3" guns for sure. But a 3"er is about taxed out pushing 1 3/4oz loads, the superheavy 2oz 3"ers even moreso. Now take that same load (or even 2 1/4oz) and push it faster with a 3 1/2" gun with about a .665"-.673" tube and see what happens. I can PROMISE you that the 3.5" will produce denser patterns and will certainly yield more knockdown at longer ranges.
But this brings me up too another point I often tell my customers. How far are you shooting turkeys? If you are absolutely sworn NOT to shoot over 40 yds then you don't even need a 3" gun. If you are sworn NOT to shoot over 50yds then you will be fine with a 3" gun. IMHO I only recommend a 3 1/2" gun and expensive tubes and lead alternative shot if you desire to cleanly kill in excess of 50yds. And another thing, when developing a longrange load you must consider the consequences of ultra-tight patterns at ranges shorter than 30 yds. I recommend body shots or "feathers only" for such guns in cases like that. You risk completely missing or just wounding a bird (with the "side" of your pattern) if you miss for some reason while taking a head/neck only shot at close range with ultra tight rigs.
Long range shotgunning isn't that different from long range riflery. Certain tools and techniques require different applications and nothing is "perfect" and all around. I have many shotguns of my own and some of my 3" guns are awfully danged good. BUT if you take the time to find that right tube and the right load I believe you will get the maximum out of your 3 1/2" 12ga that merits using them over the other two sizes of 12s!
RA
ps
As for the "detached retina" issue, I have heard that for years but I have yet to see or hear of the first documented case of it and that comes after selling 3 1/2" guns (and 10 ga.s as well) since they first came out in the late 80s! I simply think it is an "old wives tale". My 835 DOES kick harder than ANY of my big magnum rifles (with a Lazzeroni Warbird and 300 Wby being my two hardest hitting rifles) but a Simms slipover and ported Rhino tube (.695") make it very managable and it's not like you are going to be turkey round after turkey round out of it each day...