Try to progress as far as you can without upgrading the runes. When you reach the high-level stages you will be able to get 4-Star or higher runes, these are the runes you should focus on upgrading.
Elemental Advantage
Each element is strong, weak against a specific element so when you find yourself struggling in a close battle look to take elemental advantage by checking the enemy's elements and then choosing your strong element character so that you can deal extra damage.
Follow the Quests
Instead of building things up manually it is advised that you follow the quests as completing them will enable you to acquire Stealth Elf fragments, gems, red potions, scrolls, and gems.
Leader Skills
Make sure that the character you place in the first slot in team formation has a useful leader skill that will benefit the team. You will discover that most of the characters have a leader skill and you can always check to see what it is in the 'Character' menu by tapping the character followed by the skill and then the skill icon.
Natural Characters
There are several four-Star natural characters you can obtain through Adventure battles. Focus on upgrading these characters when you get them as doing so is easy.
Repeat Stages
There is no way of getting around it, to progresss in the game you will need to constantly repeat old stages over and over so you earn EXP for your team characters and soul stones so you can power-up and evolve them. EXP and soul stones can be obtained from Adventure mode battles.
Use Gems
Regularly check the mailbox or complete missions to earn gems. Then make sure you use these gems to refill energy. You can also use gems to summon but it is recommended that you instead use wish stones.
Don't Upgrade Low-Star Runes...