Want me to be honest?
For Pokémon findable in the games, go for the Pokémon yourself. If you trade, you may get a clone, but sometimes you'll find someone give you a legendary then restart to go catch it again. Some people are like that.
If you trade for those that are event-only, you better be ready to accept a clone. Many collectors with thousands of events only have thousands of events because they clone. Even with hundreds, it's only because of cloning. The exception is someone who has had the ability to acquire every single event since Generation III (usually with a very high budget for airline travel from Japan to South Korea to Taiwan to the US Gamestops to France to Germany back to Japan). And that probably doesn't exist since many are local (movie events, anyone?) and require in-person download; pre-orders for the movie tickets in Japan get you access to the many legendary Pokémon events in Japan, and those for instance will be highly sought-after. I'll consider myself extremely lucky if I even get clones of two of those myself, ever (there are six).
I myself lucked into Serena's Pancham today, myself; now I have to go find Ash's latest Pikachu from 7-11. And I'm cloning the Pancham to trade for it. And the Pikachu will be cloned. Big deal. You know how you get the event, right? It sends you a Wonder Card. There can be anywhere from 10 to 100,000 picked up, and every single one is created from scratch from the Wonder Cards. AR Wonder Cards? Legitimately downloaded Wonder Cards saved for easy pull from an AR device, and hard to identify in some cases. Ever use an AR code in Gen. IV or Gen. V? I tried a Shiny Eevee one day (and BTW, no, I have
not traded these). I got every single one with different IV spreads. It creates Pokémon from scratch. It's sad that any event generated via older AR is virtually undetectable now; I looked up dates of some older events today and there is no date in Kalos at all. I have to hope, in the future, that data returns to provide legitimacy to these again, but right now, I could import and trade a Shiny Eevee and you'd have no idea it came from an AR code. It would be unique. It would be yours alone, no clones. But it would be a hack.
So for that reason, I have no problem with clones. The events are legitimate. They have just been duplicated. It could be argued that using AR hacks to create them yourself is exactly the same thing. For that reason, I never understand the fuss. But I play the game the legal way like everyone there does. And cloning is part of the game. If you don't take event clones, you're going to have a hard time finishing your Dex for those missing few. That's how the game is played with event trading since they can never be replaced once traded away.
Shinies? Not as important, unless again it's an event clone. Tanabata Jirachi 2014. Best Jirachi ever. But some cloners see Shinies as taboo for cloning. Anything normal? Almost no point unless it's 6IV, and that's only to save you having to spend two days breeding another one for someone else. Legendaries in game? I'd clone mine, but people don't often trade for those anyway, so again there's no point. I leave mine untouched should they ever be needed. If I use one, I clone it first. I actually had Rayquaza lose to Deoxys INTENTIONALLY to not gain experience. Funny, I know, but Deoxys can be found later. Did this for Zekrom and Reshiram in Unova as well. They must hate me. LOL Ditto? Heck yeah. If you get a 6IV one, put a crown on it and have it live in the daycare. It will be your breeding superstar. If it's Shiny and foreign, clone it and flaunt it. It's very possible they are Pokégenned, but I see it as you're basically going to inbreed whatever you get anyway, so any Ditto at the start of the chain is canceled out anyway. Shane that my HA one didn't get in from Gen. V. Had to get a new one. Too bad the first was a hack.
I see what you're saying and the safeguard thing is very legit.
My overall point is that one of the biggest goals is to complete the pokedex. It's supposed to take work and cooperation between friends. However, I can literally go to the cloning thread and ask for any pokemon. That's the same as being gifted a complete pokedex. If someone were to use clones to finish off their dex, it doesn't count. Yes there are event only pokemon like genensect. The creators aren't stupid they know that. They will either release it in a another event or in-game. If they don't, they expect people to trade or trade and trade back.
I'm going to correct you here.
If you go to the cloning thread, you have to supply the Pokémon to be cloned. I'm a cloner. I don't take requests from people saying, "I need a Deoxys, can you clone one for me?" That doesn't mean I'll not be happy to give someone a cloned Deoxys (and please don't all bombard me asking now). The point of the cloning thread is that YOU already have a Deoxys to clone. We clone it for you. You can then give it to other people. How do I know this? I'm one of the cloners. We don't give people a Pokédex on request. Could I? Easily (though it would take an entire day to do it). Would I? No way. Requests have to be for Pokémon acquired by the cloner by the requesting party, and then cloned. We send both (or more) sets back. Occasionally I throw in free gifts. I'm a nice guy like that.