For your overall question, yes the choices you make can affect your gameplay. If you do enough acts of evil that are witnessed in areas then guards will attack you on site, heck even towns folk will attack you on site eventually. This can make completing any quests in those towns very difficult. Even if you are not caught the game is still aware of what is going on and you will often get snide passing remarks from the guards. I have never been spotted pick pocketing for example (my bounty level is 0). However they often threaten to make me lose my hand if they catch it in their pocket (to which I then have to steal all they have on them to prove a point, they wont catch me :)).
However, to address your second question which is hidden in the spoiler text. This is not a specific moral question in my opinion as it really comes down to how you want your character to feel about the situation. There is plenty of evidence on each side to support both of their views so neither one is truly evil or good. It just comes down to an Us or Them choice (which I skipped). There are quite a few of these set ups through out the game, the more obvious one is the Imperials vs the Storm Cloaks which my friends and I argue about all the time on which side is right :)
Is there anything that I've done incorrectly for my build, in that I shouldn't have tried to get the best gear midway through the game?
This is very subjective - what is considered an "incorrect" build by one player, may be "optimal" for another. If you want to make the game harder, focus your skill points and perks on non-combat skills: Speech, Pickpocket, Lockpicking, etc. You can also put skill points and perks on combat skills that you won't be using in combat. This will level up your character (which will make enemy level difficulty scale to your level), while at the same time, not make your character stronger for combat.
With the Dragonborn DLC installed, perks may be undone and redistributed at the cost of one dragon soul per skill tree.
At the end of the At the Summit of Apocrypha quest, you will have access to different portals (one for each skill) which allows you to clear and regain any perks in that skill tree, at the cost of one dragon soul. You remove all perks from a single skill perk tree and can use these reclaimed perks on unlocking any perks you wish, including perks taken from said perk tree. By reading the Black Book, Waking Dreams, you can return to Apocrypha and alter the skill trees whenever you wish.
Are there any hard quests that I've completely missed, or do you think that now if I start new questlines with my increased stats, the game would level up the difficulty for me?
It is subjective to state which quests are "Hard quests". Just have a look here for a list of all quests and see which ones appear to be hard for you. As for the second part of your question, the unmodded game only checks your current level and the difficulty settings in the options to compute how difficult the enemies will be for you.
Excerpts from UESP wiki's "Leveling - Effects of Leveling" article:
Various aspects of the game are leveled. This means that as your character increases in level, some enemies become more challenging but also the quality of the items you find becomes better. However, the leveling system in Skyrim has been altered from that used in Oblivion, in response to criticisms of Oblivion's leveling system.
Different locations in Skyrim have different inherent difficulties. In other words, some dungeons are designed to be too difficult for low-level characters to enter. More challenging dungeons are generally located at higher elevations, meaning that early in the game players may want to avoid mountainous regions. However, more difficult dungeons contain better rewards. In addition, some high-quality items can be randomly found even early in the game.
... Bandit NPCs are always a fixed level for their name (Bandits are level 1, Bandit Thugs are level 9, Bandit Highwaymen are level 14, etc). The player's level affects the range of possible bandit types generated within a bandit dungeon, and probably the frequency, but does not seem to affect the resulting stats except in a few rare cases. Lower variant bandits remain reasonably common even when more dangerous bandits are available.
v1.9 Patch - 'Legendary' difficulty
Patch 1.9 adds a sixth difficulty level: Legendary. It reduces damage dealt by the player to x0.25 and increases damage taken by the player to x3.
Mods
If playing on the PC, you could also make the game harder with mods:
The mod, Pluto's Improved Skyrim Experience (PISE) has a "More Intense Level Scaling" component. It makes enemies more stronger relative to your level, compared to the vanilla enemy scaling. PISE also features harder sneaking, more enemy spawns, harder enemies and an overhauled enemy AI. The mod, Path of Shadows, a major stealth overhaul mod, also makes sneaking harder.
Other mods that may make the game harder:
- DFB - Random Encounters - adds different random encounters from vanilla: Vampires, Falmers, Werewolves, Dwarven Spiders, Spheres, Centurion, etc.
- High Level Enemies - has a feature that allows certain or all enemies to scale with your level
- Deadly Dragons - overhauls dragons to make them more challenging to fight
- Balanced Magic - designed to 'balance' the game's magic spells - make the spells do damage and consume mana appropriate to your magic perks, and lessens the effect of abusive perks like the 100% stagger change of the 'Impact' perk. It also affects enemy mage NPCs, making them more challenging
- Auto-cast Racial Powers Plugin - "Auto-cast racial powers will activate for NPCs, both enemy and friendly, making fights much more interesting and adding a new element to prioritizing targets in larger fights!"
Creature mods that increase creature spawn points, number of spawns, and also improves creature AI:
(I recommend using only one creature mod, to avoid conflicts and other issues.)
Best Answer
The short answer is No, the balance of the game won't be noticeably affected.
Dawnguard introduces a few new things that modify minor aspects of the base game:
Crossbrows: Faster first shot with slower reload time. You can smith an Enhanced Version of this cross bow that ignores 50% of armor. This is pretty huge and all you need is the steel smithing perk.
The vampire and werewolf perk trees are also available, and improve the base abilities for those factions. These are gained by feasting on the flesh of your fallen foes (aka devouring a killed NPC as a werewolf or killing an NPC with drain life or bite as a vampire lord)
So what you're truly given with the DLC is some interesting build depth for players who enjoy playing as a Vampire or Werewolf, slightly more powerful weapons for those who reach 100 smithing, and a bow substitute that can eventually be improved to ignore 50% armor at high levels, but needs to be earned through Dawnguard questing.
Looking at all the info I think you can reach an objective conclusion that current players shouldn't notice any major balance upsets.