You can subclass werkzeug.serving.WSGIRequestHandler to override the behavior you don't like:
import logging
from flask import Flask
from werkzeug.serving import WSGIRequestHandler, _log
app = Flask(__name__)
@app.route('/hello')
def hello():
    return '<html><body><p>Hello, World.</p></body></html>'
class MyRequestHandler(WSGIRequestHandler):
    # Just like WSGIRequestHandler, but without "- -"
    def log(self, type, message, *args):
        _log(type, '%s [%s] %s\n' % (self.address_string(),
                                         self.log_date_time_string(),
                                         message % args))
    # Just like WSGIRequestHandler, but without "code"
    def log_request(self, code='-', size='-'):
        self.log('info', '"%s" %s', self.requestline, size)
if __name__=="__main__":
    logging.basicConfig(filename='werkzeug.log', level=logging.INFO)
    logger = logging.getLogger('werkzeug')
    logger.setLevel(logging.INFO)
    app.run(debug=True, request_handler=MyRequestHandler)
The resulting log file:
INFO:werkzeug: * Running on http://127.0.0.1:5000/
INFO:werkzeug: * Restarting with reloader
INFO:werkzeug:127.0.0.1 [30/Mar/2016 02:28:24] "GET /?foo HTTP/1.1" -
INFO:werkzeug:127.0.0.1 [30/Mar/2016 02:28:28] "GET /hello HTTP/1.1" -