If owl is such a bad play on mad scientist, why are you bringing up that?
Because you are the one who brought it up to begin with as a way to defend your stance that Mad Scientist is overrated.
You bring up all these scenarios of ways that Scientist is "bad" in and can be countered by stuff like Owl and I am saying that is not an efficient counter. Because if it was a good play then that would've deterred people from using Scientist because Owls were common.
If you Silence a Mad Scientist then you are not in a "good" position, in fact you silence Mad Scientist when you are in a bad position to begin with. Why would a Hunter play Owl on a Mad Scientist when they can play their Haunted Creeper instead? They don't. Usually Owl is the best play if you have something like a Juggler in hand and you don't want them getting free value off of it just like playing Juggler into Minibot. As a Renolock player, I don't waste my Owl on Scientist, I just tap or play Doomsayer instead or remove it with Dark Bomb. It's not a great use of my Owl at all. Against Mages it's even worse because they will just play Mana Wyrm, ping the Owl and continue to go to face. So you didn't deal with the 2/2, wasted the turn playing a 2/1 that died for free and they still have the board... you lose the game from that position in many cases.
That's like a major part of why you are saying the card is overrated.. that it gets beat by Silence and the person who silenced it is in a good position when that is not really true in practical matches.
The other reason why you stated that the card is overrated is that sometimes you get a Secret in hand and get Mad Scientist way after that. First of all... pretty much every low drop in the game is bad later on in the game. If a 2 drop isn't played in the first 5 turns then it's not going to be that good later on no matter how good the 2 drop is. Minibot isn't a great turn after turn 6 because it's low impact. Same for Zombie Chow, it's awful late in the game. So saying that Mad Scientist is mediocre because you get it later on in the game is not a good argument to make because that's how low cost cards usually work.
Now we get to the final claim on Mad Scientist which is that sometimes you get Secret first and then you get Scientist (in the first 4 turns because I have already stated how low cost cards are bad after turn 5 anyway) right after that. Unless you drew your 3 Secrets in hand and Mad Scientist... you are still very likely to have one Secret in your deck that can be pulled from Mad Scientist and that is good enough. We are talking about a very uncommon situation here where Mad Scientist might be bad because you drew all of your secrets in your opening hand.
That's equivalent to saying Dr Boom is overrated because you have a chance that the Boom Bots might hit face for 1 attack each and Doom itself gets sniped by BGH (a 3 mana BGH at that). That's again a bad argument to make and how Dr Boom was incorrectly evaluated to begin with. It's about how a card performs on average, not on fringe cases.
The times where you get those bad Mad Scientist draws are FAR OUTWEIGHED by when you play it on turn 2 and you snowball with it. It's a balancing of power and through long time trial and error the community has determined that the pros far outweigh the cons to the point that card is clearly over powered. It is over powered enough that you can afford to reduce your deck overall strength to take advantage of. That's how synergy cards work and Mad Scientist is among the strongest synergy cards in the game.
It's not like we are talking about some fringe competitive card here like Earthenring Farseer. We have mountains of data on this card at the highest levels of play. For someone to come in and claim that the card is "overrated" suggests that there is a good enough reason to not include it in your deck in some cases and I have yet to see any example where it's actually the right call to not play Mad Scientist in either Mage and Hunter. If every Hunter and Mage deck maker starts the deck by putting two Mad Scientists in without even thinking about... there is no metric by which it can be claimed that the card is overrated unless the barometer is "play Mad Scientist on turn 2 = automatic win". By that measure, you can say that Tuskar Totemic was overrated because it didn't always win you the game on turn 3. If Mad Scientist was in Standard right now then it would've been nerfed a long time ago.