Paul,

I feel your pain, after deploying multiple communities that have implemented both the PKB, and Chatter Answers, it is a difficult toss up.  Short answer, roll your own.  if you have a Force.com site being run by VF pages,  go ahead and create the necessary pages to display your article and category lists using the <knowledge: VF elements available. If you have concerns on how to display a proper navigation based on the Data Categories, I acutally had to create a JSON output representing the Categories in my Page Controller, and then on the front end, I used a Javascript library (pick one  - javascript, angularJS  - whatever) to render the navigation dynamically from the JSON String exposed as a public variable.  Below is a sample of code I used to do that.... took me a minute to figure it out....

/**
	 * This method is designed to get a hierarchal represnetation of the Data Categories assigned to 
	 * knowledge articles. 
	 *
	 * @param categoryGroupName - the Category Group to Get the Data FROM
	 * @param categoryName - the Name to consider as the Top level Category. Will not be included in output.
	 * @return String - the resulting Data Category Structure in JSON Format.
	 **/
	public static String GetDataCatetgoryInformation(String categoryGroupName, String categoryName)
	{
		String jsonString;
		Schema.DataCategoryGroupSobjectTypePair startingPair = new Schema.DataCategoryGroupSobjectTypePair();
		startingPair.setDataCategoryGroupName(categoryGroupName);
		startingPair.setSObject('KnowledgeArticleVersion');
		List<Schema.DescribeDataCategoryGroupStructureResult>results = Schema.describeDataCategoryGroupStructures(new Schema.DataCategoryGroupSobjectTypePair[]{startingPair},false);
		System.debug(LoggingLevel.INFO,'\n*****\n Group Structure Result: ' + results[0] + '\n*****\n\n');
		List<Schema.DataCategory> allList = results[0].getTopCategories();
		Schema.DataCategory allCat = allList[0];
		System.debug(LoggingLevel.INFO,'\n*****\nChild Categories of all: ' + allCat.getChildCategories() + '\n*****\n');
		List<Schema.DataCategory> ts360CatList = allList[0].getChildCategories();
		System.debug(LoggingLevel.INFO,'\n*****\n ts360CatList: ' + ts360CatList + '\n*****\n');
		Schema.DataCategory startingCategory;
		for(Schema.DataCategory category:ts360CatList){
			if(category.getLabel() == categoryName){
				startingCategory = category;
				break;
			}
		}
		if(startingCategory != null && startingCategory.getChildCategories().size() > 0){
			JSONGenerator jsonCategoryListing = TS360ComKnowledgeExtension.JSONifyCategoryNames(JSON.createGenerator(false), startingCategory.getChildCategories()) ;
			jsonCategoryListing.close();
			jsonString = jsonCategoryListing.getAsString();
			System.debug(LoggingLevel.INFO,'\n*****\n JSON Information: ' + jsonString + '\n*****\n');
		} else {

			System.debug(LoggingLevel.INFO,'\n\n*****\n Starting Categories might be empty:\n*****\n');
		}

		return jsonString;
	}



private static JSONGenerator JSONifyCategoryNames(JSONGenerator gen, List<Schema.DataCategory> dcList){
		try{
			gen.writeStartArray();
			for(Schema.DataCategory dc:dcList){
				gen.writeStartObject();

				gen.writeStringField('label',dc.getLabel());
				gen.writeStringField('name',dc.getName());
				if(dc.getChildCategories().size() > 0){
					gen.writeFieldName('children');
					gen = TS360ComKnowledgeExtension.JSONifyCategoryNames(gen,dc.getChildCategories());
				}

				gen.writeEndObject();
			}
			gen.writeEndArray();
		}catch(System.Exception ex){
			System.debug(LoggingLevel.INFO,'\n******\nError: ' + ex.getMessage() + '\n*****\n\n');
			throw ex;
		}
		return gen;
	}

As far as the chatter Answers portion of the Communities, I simply used the <chatteranswers: elements which work pretty well and stay self contained.  My only warning on using these elements is that sometimes your page formatting can screw up these displays, so be careful about your CSS structure. Jsut remember that in using these elements, the documentation says pass in the communityId, but you must pass in the ZONE ID of the Zone assigned to the Community.

Why use both?  Because Answers has the unique benefit of providing users the capability to ask a question to the community, if they can't find it in the Knowledge or if it already hasn't been asked.  Knowledge however, can be much more structured that Answers.  My clients wanted the best of both worlds.

You final option would be to utilize the Site.com 'Community Templates' offered in the new Spring '15 implementations of Communities.  They are very nice - and offer great examples of a SPA App (Single Page Application) - but they ARE NOT MODIFIABLE - that sucks... Great examples though of what cold be put together with some ingenuity.

Hope this helps.  You question is kind of subjective, but if I was able to answer your questions, please mark this reply as 'Solved'.

Thanks!