How might Runes negatively affect playstyles and non-meta pick?

The old rune system had something to say when it came to play styles and picks, something which the new system seems to pull away from. Often when playing a role your champion isn't suited for you often need to tweak your runes for optimization for that unusual role, it's a fine tuning process in for every match up for every lane. But under the new system is seam more difficult to tune your runes. For example non-meta junglers being one of the more popular roles that can take a great amount of tuning to first off, survive in the jg, secondly the clear, and finally to gank lanes. Inability to do one of these can negatively impact the game. And to compensate you can end up with some weird solution utilizing runes as they will most affect your early game potential and set your pace. For example many mages don't suit the role of a jg'er, one reason being is high mana cost. From this you can either attempt an AD start, or put some runes into mana regen. And likely you don't want to sacrifice to much of your other stats so you may only put 3 or 4 runes for that category, something the new system doesn't allow with it's limited options and space. This lack of options and versatility affects how laning might go as well. As sometimes you'll see high damage runes for the sake of early kills and trade, or more defensive pages to defend yourself against champions/matchups you struggle against.