As per my experience, WordPress & WooCommerce Affiliate Program is the best WordPress plugin for implementing the affiliate system as well as MLM(Multi-Level Marketing) on your WordPress website. The main thing is that all features of this plugin is working. The author team provides very fast and good support. Another Main thing is that they have mentioned on their product page they will launch a Native Android and iOS App for WooCommerce which is fully compatible with this plugin that will be a great thing.
Some main features which I like are:
Two Way Commission - Give commission to affiliate and also give discounts to users.
Multi-Level Marketing ( MLM ) - Binary, Forced Matrix, Unilevel
Manual Referral/Commission
Social Media Share
Automatic Banner Generation, even generate QR code of link and many more affiliate tools to market your products
SignUp Bonus and Performance Bonus
Lifetime / Unlimited Commission
Coupons – Affiliates can generate coupons
Different Templates for Login and Signup

I've successfully helped over 150 entrepreneurs, startups, and businesses, and I would be happy to help you. Please send me more information before scheduling a call - so I can give you maximum value for your money. Take a look at the great reviews I’ve received: https://clarity.fm/ripul.chhabra