I think I agree that they shouldn't generally be played together. I just have trouble making sense of everyone's love for Shaymin EX. It seems like more of niche play in particular decks as opposed to him being splashable in every deck as an alternative to draw supporters (which seems like a lot of people's intention. Correct me if I'm wrong). I just don't believe people will want multiples of these clogging up their benches, especially when they have no intention of attacking with him. While Super Scoop Up has proven to be a very competitive card, Toad-lock isn't going away, so there isn't going to be a reliable way to get these things back into your hand. I still feel like Jirachi is the more reliable choice while also offering the diversity you need in a specific situation.
I think Shaymin's hype is completely justified after some initial testing, but that people are hyping it for the wrong reasons. Like you, i've heard people talking about it in a sense of replacing draw supporters. I believe that shouldn't be the case though.
The brilliance of it, is being able to Lysandre and play shaymin to draw cards in the same turn. OR say in a fighting deck, Korrina for Fighting pokemon + ultra ball, ultra ball for shaymin, shaymin to draw up to 6. Let's say Teammates for Shaymin + Strong energy? then Shaymin to draw. Even just to N/Colress for low amounts and still get a decent draw out of it, or being able to play down a big hand, then Shaymin for draw, and then being able to draw a second time (or multiple times depending on deck) It really makes all the difference in those situations, I think people will begin to realise as it's being used.
If using it with Sky Field you can also discard them when skyfield is removed, meaning they aren't a target anymore and if you run trump card you can Trump + Ultra Ball for more draw support as well as recycling your discard.
Using it with Bats is nice because you can cycle through your deck faster to get those evolutions and you already run scoop ups.
It's a versatile card, but the bonus imo is that it doesn't affect your supporters. With Jirachi you have to remove a potentially valuable supporter from your deck and then use your supporter for that turn too to make its ability useful. Whereas with shaymin you have less variety but more consistency, being able to jirachi for a Lysandre is nice but purely because of the pain of drawing dead, i'm going to be using shaymin.