There are a number of Pok?mon whose middle evolutions I prefer over the final evolutions for one reason or another, though these reasons are rarely ever sufficient to keep me from evolving them anyway since I always raise my Pok?mon to their fullest extent if I'm bothering to use them on a team.
Haunter
Back in the day, I never really had easy access to trading so I had to live with Graveler, Haunter, Kadabra, and Machoke instead of Golem, Gengar, Alakazam, and Machamp. While I now prefer Golem, Alakazam, and Machamp over their middle-stages, I still like Haunter a bit better than I do Gengar. Gengar's not bad, I'll use a Gengar and be perfectly content, but Haunter has those cool disembodied hands and its design feels a bit more jagged, rough, and spooky. Just seems a bit cooler to me to this day.
Dragonair
Dragonair looks far better than Dragonite and, while I like Dragonite, it's a shame that they didn't keep the design consistent for the final evolution of that line and made Dragonite either its own Pok?mon or the final evolution of some other line. Dragonair either evolving into something keeping the same aesthetics as Dratini and Dragonair, or being Dratini's final evolution and having higher stats to compensate for that, would be best.
Togetic
I like Togekiss, it's not bad, but it feels like a strange progression from Togetic. I also have years more of affection for Togetic since it was present in Gold & Silver.
Flaffy
Like Togekiss above, I've always liked Ampharos since I first encountered it in Gold & Siler, but Ampharos bears barely any resemblance to its Mareep origins. Flaffy still maintains a sheepish appearance, and I like the pink coloration with the blue tail orb. I'll use Ampharos over Flaffy any day of the week because of the stats and Mega Evolution, but Flaffy wins handily in the design department.
Marill
The design is simply way more appealing than Azumarill to me. Mostly just my nostalgia talking though, because Marill stood out a bit back in the pre-Gold & Silver days. I never believed the "Pikablue" rumor but I still liked it.
Grovyle
Sceptile is a great Pok?mon and I'll use it, but Grovyle wins out here simply because when I look at Sceptile and see the seeds on its back it just makes me think of back acne and that's not a good look at all. I always get over that and use Sceptile anyway, but yeah.
Vigoroth
One of the few Pok?mon that I will purposefully leave unevolved. Slaking is cool and I'll use both Slaking and Vigoroth, but I'll take the hit in stats to actually be able to use my Pok?mon in battle in every turn.
Dusclops
I like Dusknoir, but its design doesn't really compare to Duskull and Dusclops. I prefer the mummyesque design and Eviolite takes its ridiculously high defenses even higher. I'll still evolve some Dusclops into Duknoir if I want to hit back harder, but eh. Like Vigoroth, Dusclops is a Pok?mon that I will happily keep unevolved on a team.
Dewott
I see what they were going for with Samurott but Dewott is the best Pok?mon in this evolutionary line for me.
Oh, and these barely count, but:
Porygon2
I like both Porygon2 and Porygon-Z, but Porygon-Z's "corrupted" appearance isn't all that crazy looking. Porygon2 has a nicer design and isn't wholly worthless in comparison because it has access to Eviolite, so what it lacks in power and speed compared to Porygon-Z, it makes up for in its Eviolite-boosted defenses. Like Vigoroth earlier, I like to use both Porygon2 and Porygon-Z and they're on pretty equal footing for me due to their individual strengths.
Finally, I prefer Charizard, but I just want to give acknowledgement to Charmeleon. I love the name, its design, while simple, is nice enough, and I've always liked it. I'd say it would probably be my favorite middle evolution of all the starters, though it has competition from Dartrix.
