The two most commonly-used cards from that set on its release were easily Gravekeeper's Commandant (Rare, meaning one per pack) and Raiza the Storm Monarch (Super Rare, one per five packs). Volcanic Doomfire, Ultra Rare (one per 24 packs) cover card for Force of the Breaker, requires a card that requires another card that are both only useful with a bunch of other cards, leading to it being played rarely.
Archetype boss monsters in general fell into this, especially during the GX era, where Awesome, but Impractical was pretty much the norm.
Venominaga however can only be played with Venominion's ability (with almost no exception), so even if you do score this extremely-rare card, there's no way you can play it unless you shell out the money for the other, or get lucky with the pack again. Venominion and Venominaga are good examples, with one being Ultra Rare and the other being Secret Rare. This can be worse if the "summoning" card is a rare in of itself. Pretty much any card that requires another card to play.And if you actually manage to do that, due to the aforementioned monsters' effects it's far more sensible to keep them on the field rather than waste them to summon Gate Guardian. Useless unless you also have Sanga of the Thunder, Suijin and Kazejin (which are themselves pretty rare) and have them all on the field at the same time.
The Star Wars Customizable Card Game has Epic Events, which typically require not only that you use associated cards, but your opponent use associated cards for instance, Attack Run depends on your opponent using the Death Star and you having Death Star: Trench and Proton Torpedoes.And the designers can't just stick all the "good" cards in rare they want to avoid Power Equals Rarity and have some of the good stuff available in common and uncommon as well.Or if some cards of a cycle have to be rare, then the remaining ones should be rare too. If there are too many uncommons in a set, some cards have to be bumped up to rare. Ironically, that means that rare cards are more likely to be "not for you", since they don't want to put such cards at lower rarities where they'll annoy more people. If a card is too niche or too powerful for game formats with more limited card pools, then they're made rare to limit the disruption.Big, impressive, and/or unique creatures and spells are rare in order to keep them special.The creators eventually instituted design rules to specifically cut down on how much complexity can appear on common cards in order to keep them newbie-friendly. Cards that are complicated in some way (like weird rules interactions or even just a Wall of Text) are rare in order to avoid overwhelming beginner players with advanced concepts.Necropotence is banned in most formats as it broke the Meta.) (Example: Necropotence was considered a useless card until a couple of players realized that one card is worth a lot more than one life, and the only life that counts is your last one. Some people even like "bad" cards for the puzzle of trying to make them work - and sometimes they succeed and prove they were never "bad" after all. Magic has a lot of demographics to cater to, so not all cards will be a good match for everyone. First of all, maybe they're not objectively "bad", they're just not for you.Mark Rosewater, the game's head designer, wrote lengthy defenses of the practice titled "When Cards Go Bad" (about how "bad" cards get made, regardless of rarity), "Rare, but Well Done", and "The Good, the Bad and the Ugly Truth" in which he discusses in great detail why "bad" cards can be designated rare: Magic: The Gathering has a lot of these, usually on purpose.