I just went through this process over the last year. If you are going to build a bike, do so such that the end result is a work of art. Something that is pragmatic, provides a comfortable, zen-like riding experience, and is still suitable to hang on one's wall and admire when the weather outside is frightful.
A couple of things:
1. If you don't like sloping top tubes, then whatever you do, do not settle for a frame with a sloping top tube. Otherwise, every time you look at the bike you are going to go "ewwww" and wished you stuck to your guns. I made the mistake once, and never plan to do it again. The same goes for threaded headsets and quill stems. If you like this aesthetic, do not settle.
I really like the standard level top tubes. Grew up with them and love the looks.
2. Racks are lame. They add weight and they ruin the lines on a bike. You don't need them either, unless this is a grocery getter. Instead, find a way to attach a saddle bag to your saddle that you can quickly remove. There are posts on this site on ways to attach hooks to a bag, which will hook into saddle loops. If your saddle doesn't have loops, you can buy bolt-on ones from Velo Orange. A Carradice Barley will hold a six pack of tall boys with still room to spare for a mini U-lock, phone, wallet, keys, tools, etc. You can also attach a shoulder strap to it, so you can comfortably carry it around when you have your bike locked up. One of the advantages to saddle bags is that you can buy multiple sizes of bags for different types of riding excursions, so that you are never carrying around more weight/bulk than you need to. They also look cool if they are made of canvas and leather. Extra items can be carried in a shoulder bag when needed. If you need to carry bigger items, get a small rack for the front of the bike that you can quickly attached/detach a basket to. The front rack also gives you something to bolt a light to if you do decide to go with a front generator hub. The SON stuff is pretty cool.
I like a rack for the looks, but there are times when I take it off and just leave the fenders on and the bike looks more like yours (less the straight top tube). I do like the idea of a rear bag for most riding though. Just not sure I could do the long distance stuff with rear bag and small front rack. I'm up to the challenge though. Spent three days in the cold desert with only a 26 liter pack. Fasting though so no need to carry food
3. Fenders are really a must, even if they do dowdify and domesticate one's build. One way to minimize the aesthetic hit, and possibly even improve aesthetics, is to get the fenders (either aluminum or stainless steel, really should be stainless steel though, they are worth the weight) painted the same color as your frame. If you can get stripes (penstripes and/or rally stripes) painted on as well, well now you are cooking. I made the mistake of being too impatient to have the frame builder paint me a pair of fenders before sending me my frame. Still planning on eventually trying to match the frame paint and paint them myself, but I doubt the results are going to look as good. Do not get plastic fenders. Just don't. Think long and hard about wood fenders before buying. Some look pretty nice on paper, but the weight hit and the lack of a curved sectional profile could ruin your lines. They may also start to look long in the tooth fairly quickly if your bike will see adverse weather frequently.
Agreed, agreed, agreed!
4. Belt drive and other new-fangled contraptions - Really research this stuff ad nauseam. Especially if it is something you can't change out if you decide you don't like it without getting a new frame. Personally, I would just stick with tried and true chains, and tech that is at least 10 years old like square taper BB's.
Belt drive is pretty cool, but I probably would be fine with a chain. I just want to ensure that the frame can be split of course if I go with a belt.
5. IGH - I am a big fan of IGH's. There is a weight penalty, but it is not much, and they keep lines on one's build simple. With bikes I find that simple always equals grace and beauty (i.e. track bikes). Don't go with anymore gears than you need, as the higher geared IGH's start to look clunky. I am quite fond of coaster brake models as you don't have to clutter up the rear half of the bike with a brake and cable, and still have the same amount of braking power on the rear in any weather/riding conditions.
I haven't added up the cassette, rear derailleur, front derailleur, double or triple cranks, cables, shifters (for front) etc. vs. an IGH, but like you say, probably not much of a penalty.
6. Tires - Aim for 32mm, give or take. Don't cheap out. Depending on the level of flat protection you need, get as supple of a tire as you can afford. Grand Bois, Jack Browns, Paselas, Vittoria Voyager Hypers, and my favorite, Challenge Strada Biancas should all be good options.
Not sure I'd want to go back to anything less than 32, but prefer 35mm wide Schwalbe Marathon Supremes.
7. Handlebars - Flat bars or north roads can be what ties the build together, but they also limit you on range. I find with flat bars and good padded gloves (talking gel), I can go for about 10 miles before I need to stop a bit to give my hands a rest. I am an old man though, so take this with a grain of salt. Not a problem if you are doing a leisurely day ride, stopping for drinks/food and photos every so often. If you are going to take this out on the highway and put on some miles, get drop bars. With flat bars, the type of grips can make a big difference. Get as much shock absorption as you can afford cost and aesthetic wise.
Shallow drops for me. Riding on the hoods most, but when I go to the tops I feel very relaxed. To the drops in wind only.
8. Accent color - The color of all the stuff that gets attached to the bike. Silver is usually the safest and best bet here for metal components, but if you decide to go with another color, make sure you can get all your components in that color. Metal components should all be one color, leather and plastic/synthetic components should also match. You will find that I violate this rule with my grips and saddle at the link below, and I think you will agree it is unfortunate. This takes a lot of planning, so think before you buy.
Like the bare look of SS or Ti. Would accent with black (or other color) fenders.
9. Lastly and most importantly - When considering any component, do a Google and Flickr image search, to see how things look and work out on a frame. Many times, you see the part by itself and think that would be nice to have, but when it gets bolted to a frame, you realize the dimensions are all off, or it just doesn't work the way you envisioned in your head. This is the only way to narrow down handlebar options, and even then, there is still going to be some trial and error.
My latest build at the link below is a fair example, in my opinion anyway, of what I am talking about. I have replaced the tires, am planning on replacing the grips, and need to paint the fenders, but otherwise this fits my needs to a T. If you click on the photo, you see the component list out, if you happen to be curious.
http://www.flickr.com/photos/98072004@N04/9512191955/