Generally it's not that bad but there are some inconveniences:
- When Kongregate is down I cannot play the game.
- Kongregate doesn't use encrypted connection (HTTPS), so the account is less secure. Security is not a big issue for someone who plays flash games casually. However, RotMG accounts may be worth hundreds of dollars.
- I cannot use the Kong name glitch to make myself unnamed or change name for free.
- The "secret" (equivalent of password) does not change. Changing Kongregate password changes the auth token for the loader but the "secret" credentials remain the same. That means if your account is compromised - it will stay compromised. There are cases of people who got hacked repeatedly after they linked to Kongregate. Changing their password didn't help because the hackers could still access the account through Kongregate.
- Kongregate site has flash ads that eat processor power and may cause lag. Fortunately they can be blocked. Also a flash projector can be used with Kongregate account, without entering Kong website. However that may change in the future.
- At some point you may want to sell your account. Selling the RotMG account created at Kongregate may be complicated or impossible without selling also the whole Kongregate account that may have other games linked and invested in, plus all Kongregate progress (rank, badges, uploads, forum posts, friends, followers, etc.)
- E-mail is not displayed in main menu, the Kongregate username is displayed instead. That may be convenient for people who stream their gameplay / make videos.
- Kongregate chat. I don't need it but for some people use it.
Protip: create your main account at www.realmofthemadgod.com. Avoid Kongregate, Steam and Kabam sites and investing into accounts created there.