There are some underrated Pokemon I can think of up the top of my head that I come to love after using them. This might take a long time lol.
First off is Cradily. Now I was one of those people who liked Armaldo better because it was more offensive. While I still really like it, I think Cradily is a lot better. It is a very defensive Pokemon and can keep restoring health with moves like Ingrain. If you don't know what you're doing against this thing, kiss your victory goodbye because it can potentially sweep an entire team of Pokemon. Also I like the unique typing.
Next is two of the eeveeloutions, Leafeon and Flareon. People have been saying how bad Flareon is because of its highest stat being attack. I think people are forgetting its 95 BASE SPECIAL ATTACK which is still very good. Plus its base 110 Special Def. is the highest out of all non legendary fire type Pokemon. Using one in XD right now and it KOs everything, even water types. As for Leafeon, I'd used one in competitive battling and it served me well. It's a very fun Pokemon to experiment with. You can teach it Swords Dance with Baton pass, have a sun setter on your team and teach Leafeon Synthesis and let it have its hidden ability Chloraphyll, and other options to explore. Both of their designs are adorable as well.
Then there are two starters i find underrated, and they are Meganium and Emboar. Now people hate on Emboar for its design and typing. I personally like the design and even though its the third fire/fighting, there have been three mono grass and water starters and no one cared. The only negative thing i can think of is not learning enough fighting moves leveling up, but other than that its still a good Pokemon. Meganium now is a Pokemon I feel doesn't get the attention it deserves. It's suppose to be a defensive/supportive Pokemon and does a really good job at it. It has access to moves like Reflect, Light screen, Aromatherapy, and even Dragon Tail if you have any entry hazards set up. As for using it in your Johto journeys, it can help take out the gym leader's Pokemon that are a threat including Whitney's Miltank and Clair's Kingdra. Plus, Meganium is very cute and has a care free nature which is very charming.
Now to keep this post for going to long I'll just say what others i find unloved quickly.
Grumpig, Venomoth, Musharna, Venasaur, Ariados, Bronzong, Jellicent, Lanturn, Vivillion, Swalot, Dunsparce, Hypno, Dodrio, Arceus, Castform, Wobbuffet, Miltank, Vileplume, Ferrothorn, and last but not least Bastidon.