They've definitely upped the difficulty over time. Enemy fire is more accurate, sometimes minibosses will spawn in during alerts, and more nullifier (power negating bubbles) and eximus units (elites) throughout. But you also have a lot more mobility you can use in defense, and more status based weapons you can utilize (to proc fire, viral, corrosive, etc.)
In the meanwhile Trinity's link (damage reflection) can really turn the tide. Energy vampire can keep you juiced up at all times, and well timed Blessings can keep you in the fight.
Yeah I am not using her abilites well I geuss.
Also I am currently getting disconnected all the time so I can't make any progress :-(